Inferences on population history of a seed chalcid wasp: invasion success despite a severe founder effect from an unexpected source population

Most invasive species established in Europe originate from either Asia or North America, but little is currently known about the potential of the Anatolian Peninsula (Asia Minor) and/or the Near East to constitute invasion sources. Mediterranean forests are generally fragile ecosystems that can be threatened by invasive organisms coming from different regions of the Mediterranean Basin, but for which historical data are difficult to gather and the phylogeographic patterns are still poorly understood for most terrestrial organisms. In this study, we characterized the genetic structure of Megastigmus schimitscheki, an invasive seed‐feeding insect species originating from the Near East, and elucidated its invasion route in South‐eastern France in the mid 1990s. To disentangle the evolutionary history of this introduction, we gathered samples from the main native regions (Taurus Mountains in Turkey, Lebanon and Cyprus) and from the invaded region that we genotyped using five microsatellite markers and for which we sequenced the mitochondrial Cytochrome Oxidase I gene. We applied a set of population genetic statistics and methods, including approximate Bayesian computation. We proposed a detailed phylogeographic pattern for the Near East populations, and we unambiguously showed that the French invasive populations originated from Cyprus, although the available historical data strongly suggested that Turkey could be the most plausible source area. Interestingly, we could show that the introduced populations were founded from an extremely restricted number of individuals that realized a host switch from Cedrus brevifolia to C. atlantica. Evolutionary hypotheses are discussed to account for this unlikely scenario.     

Balancing bioenergy and biosecurity policies: estimating current and future climate suitability patterns for a bioenergy crop

In an apparent paradox, bioenergy crops offer potential benefits to a world adjusting to the challenges of climate change and declining fossil fuel stocks, as well as potential ecological and economic threats resulting from biological invasions. In considering this paradox it is important to understand that benefits and threats may not always be apparent in equal measure throughout the potential range of each candidate biofuel species. In some environments, a species could potentially produce valuable biological materials without posing a significant invasion threat. In this study, we develop a bioclimatic niche model for a candidate biofuel crop, Millettia pinnata, and apply the model to different climatic and irrigation scenarios to estimate the current and future patterns of climate suitability for its growth and naturalization. We use Australia as a case study for interpreting the niche model in terms that may be informative for both biofuels proponents and biosecurity regulators to plan management programmes that reflect the invasive potential in different areas. The model suggests that suitable growing conditions for M. pinnata in Australia are naturally restricted to the moist and semimoist tropics. Irrigation can extend the suitable growing conditions more widely throughout the tropics, and into more arid regions. Under future climate scenarios, suitable growing conditions for M. pinnata under natural rainfall contract towards the east coast, and extend southward into the subtropics. With irrigation, M. pinnata appears to have the potential in the future to naturalize across much of Australia. The bioclimatic modelling method demonstrated here is comparatively quick and easy, and can produce a rich array of data products to inform the interests of both bioenergy proponents and biosecurity regulators. We show how this modelling can support the development of spatially explicit biosecurity policies designed to manage invasion risks in a manner that balances bioenergy and biosecurity concerns.     

related: an R package for analysing pairwise relatedness from codominant molecular markers

Analyses of pairwise relatedness represent a key component to addressing many topics in biology. However, such analyses have been limited because most available programs provide a means to estimate relatedness based on only a single estimator, making comparison across estimators difficult. Second, all programs to date have been platform specific, working only on a specific operating system. This has the undesirable outcome of making choice of relatedness estimator limited by operating system preference, rather than being based on scientific rationale. Here, we present a new R package, called related, that can calculate relatedness based on seven estimators, can account for genotyping errors, missing data and inbreeding, and can estimate 95% confidence intervals. Moreover, simulation functions are provided that allow for easy comparison of the performance of different estimators and for analyses of how much resolution to expect from a given data set. Because this package works in R, it is platform independent. Combined, this functionality should allow for more appropriate analyses and interpretation of pairwise relatedness and will also allow for the integration of relatedness data into larger R workflows.     

Seed dispersal and realized gene flow of two forest orchids in a fragmented landscape

• Species with vast production of dust‐like windborne seeds, such as orchids, should not be limited by seed dispersal. This paradigm, however, does not fit recent studies showing that many sites suitable for orchids are unoccupied and most seeds land close to their maternal plant. To explore this issue, we studied seed dispersal and gene flow of two forest orchid species, Epipactis atrorubens and Cephalanthera rubra, growing in a fragmented landscape of forested limestone hills in southwest Bohemia, Czech Republic.
• We used a combination of seed trapping and plant genotyping methods (microsatellite DNA markers) to quantify short‐ and long‐distance dispersal, respectively. In addition, seed production of both species was estimated.
• We found that most seeds landed very close to maternal plants (95% of captured seeds were within 7.2 m) in both species, and dispersal distance was influenced by forest type in E. atrorubens. In addition, C. rubra showed clonal reproduction (20% of plants were of clonal origin) and very low fruiting success (only 1.6% of plants were fruiting) in comparison with E. atrorubens (25.7%). Gene flow was frequent up to 2 km in C. rubra and up to 125 km in E. atrorubens, and we detected a relatively high dispersal rate among regions in both species.
• Although both species occupy similar habitats and have similar seed dispersal abilities, C. rubra is notably rarer in the study area. Considerably low fruiting success in this species likely limits its gene flow to longer distances and designates it more sensitive to habitat loss and fragmentation.

     

Development and validation of microsatellite markers for Karnal bunt (Tilletia indica) and loose smut (Ustilago segetum tritici) of wheat from related fungal species

Simple sequence repeats (SSRs) are preferred molecular markers because of their abundance, robustness, high reproducibility, high efficiency in detecting variation and suitability for high‐throughput analysis. In this study, an attempt was made to mine and analyse the SSRs from the genomes of two seed‐borne fungal pathogens, viz Ustilago maydis, which causes common smut of maize, and Tilletia horrida, the cause of rice kernel smut. After elimination of redundant sequences, 2,703 SSR loci of U. maydis were identified. Of the remaining SSRS, 44.5% accounted for di‐nucleotide repeats followed by 29.8% and 2.7% tri‐ and tetranucleotide repeats, respectively. Similarly, 2,638 SSR loci were identified in T. horrida, of which 20.2% were di‐nucleotide, 50.4% tri‐ and 20.5% tetra‐nucleotide repeats. A set of 65 SSRs designed from each fungus were validated, which yielded 23 polymorphic SSRs from Ustilago and 21 from Tilletia. These polymorphic SSR loci were also successfully cross‐amplified with the Ustilago segetum tritici and Tilletia indica. Principal coordinate analysis of SSR data clustered isolates according to their respective species. These newly developed and validated microsatellite markers may have immediate applications for detection of genetic variability and in population studies of bunt and smut of wheat and other related host plants. Moreover, this is first comprehensive report on molecular markers suitable for variability studies in wheat seed‐borne pathogens.     

Managing diversity: Domestication and gene flow in Stenocereus stellatus Riccob. (Cactaceae) in Mexico

Microsatellite markers (N = 5) were developed for analysis of genetic variation in 15 populations of the columnar cactus Stenocereus stellatus, managed under traditional agriculture practices in central Mexico. Microsatellite diversity was analyzed within and among populations, between geographic regions, and among population management types to provide detailed insight into historical gene flow rates and population dynamics associated with domestication. Our results corroborate a greater diversity in populations managed by farmers compared with wild ones (H_E = 0.64 vs. 0.55), but with regional variation between populations among regions. Although farmers propagated S. stellatus vegetatively in home gardens to diversify their stock, asexual recruitment also occurred naturally in populations where more marginal conditions have limited sexual recruitment, resulting in lower genetic diversity. Therefore, a clear‐cut relationship between the occurrence of asexual recruitment and genetic diversity was not evident. Two managed populations adjacent to towns were identified as major sources of gene movement in each sampled region, with significant migration to distant as well as nearby populations. Coupled with the absence of significant bottlenecks, this suggests a mechanism for promoting genetic diversity in managed populations through long distance gene exchange. Cultivation of S. stellatus in close proximity to wild populations has led to complex patterns of genetic variation across the landscape that reflects the interaction of natural and cultural processes. As molecular markers become available for nontraditional crops and novel analysis techniques allow us to detect and evaluate patterns of genetic diversity, genetic studies provide valuable insights into managing crop genetic resources into the future against a backdrop of global change. Traditional agriculture systems play an important role in maintaining genetic diversity for plant species.     

Whitebark pine facilitation at treeline: potential interactions for disruption by an invasive pathogen

In stressful environments, facilitation often aids plant establishment, but invasive plant pathogens may potentially disrupt these interactions. In many treeline communities in the northern Rocky Mountains of the U.S. and Canada, Pinus albicaulis, a stress‐tolerant pine, initiates tree islands at higher frequencies than other conifers – that is, leads to leeward tree establishment more frequently. The facilitation provided by a solitary (isolated) P. albicaulis leading to tree island initiation may be important for different life‐history stages for leeward conifers, but it is not known which life‐history stages are influenced and protection provided. However, P. albicaulis mortality from the non‐native pathogen Cronartium ribicola potentially disrupts these facilitative interactions, reducing tree island initiation. In two Rocky Mountain eastern slope study areas, we experimentally examined fundamental plant–plant interactions which might facilitate tree island formation: the protection offered by P. albicaulis to leeward seed and seedling life‐history stages, and to leeward krummholz conifers. In the latter case, we simulated mortality from C. ribicola for windward P. albicaulis to determine whether loss of P. albicaulis from C. ribicola impacts leeward conifers. Relative to other common solitary conifers at treeline, solitary P. albicaulis had higher abundance. More seeds germinated in leeward rock microsites than in conifer or exposed microsites, but the odds of cotyledon seedling survival during the growing season were highest in P. albicaulis microsites. Planted seedling survival was low among all microsites examined. Simulating death of windward P. albicaulis by C. ribicola reduced shoot growth of leeward trees. Loss of P. albicaulis to exotic disease may limit facilitation interactions and conifer community development at treeline and potentially impede upward movement as climate warms.     

Using neutral cline decay to estimate contemporary dispersal: a generic tool and its application to a major crop pathogen

Dispersal is a key parameter of adaptation, invasion and persistence. Yet standard population genetics inference methods hardly distinguish it from drift and many species cannot be studied by direct mark‐recapture methods. Here, we introduce a method using rates of change in cline shapes for neutral markers to estimate contemporary dispersal. We apply it to the devastating banana pest Mycosphaerella fijiensis, a wind‐dispersed fungus for which a secondary contact zone had previously been detected using landscape genetics tools. By tracking the spatio‐temporal frequency change of 15 microsatellite markers, we find that σ, the standard deviation of parent–offspring dispersal distances, is 1.2 km/generation^1/2. The analysis is further shown robust to a large range of dispersal kernels. We conclude that combining landscape genetics approaches to detect breaks in allelic frequencies with analyses of changes in neutral genetic clines offers a powerful way to obtain ecologically relevant estimates of dispersal in many species.     

Host specificity and reproductive success of yucca moths (Tegeticula spp. Lepidoptera: Prodoxidae) mirror patterns of gene flow between host plant varieties of the Joshua tree (Yucca brevifolia: Agavaceae)

Coevolution between flowering plants and their pollinators is thought to have generated much of the diversity of life on Earth, but the population processes that may have produced these macroevolutionary patterns remain unclear. Mathematical models of coevolution in obligate pollination mutualisms suggest that phenotype matching between plants and their pollinators can generate reproductive isolation. Here, we test this hypothesis using a natural experiment that examines the role of natural selection on phenotype matching between yuccas and yucca moths (Tegeticula spp.) in mediating reproductive isolation between two varieties of Joshua tree (Yucca brevifolia var. brevifolia and Y. brevifolia var. jaegeriana). Using passive monitoring techniques, DNA barcoding, microsatellite DNA genotyping, and sibship reconstruction, we track host specificity and the fitness consequences of host choice in a zone of sympatry. We show that the two moth species differ in their degree of host specificity and that oviposition on a foreign host plant results in the production of fewer offspring. This difference in host specificity between the two moth species mirrors patterns of chloroplast introgression from west to east between host varieties, suggesting that natural selection acting on pollinator phenotypes mediates gene flow and reproductive isolation between Joshua‐tree varieties.     

Understanding the mechanisms of antitropical divergence in the seabird White‐faced Storm‐petrel (Procellariiformes: Pelagodroma marina) using a multilocus approach

Analytical methods that apply coalescent theory to multilocus data have improved inferences of demographic parameters that are critical to understanding population divergence and speciation. In particular, at the early stages of speciation, it is important to implement models that accommodate conflicting gene trees, and benefit from the presence of shared polymorphisms. Here, we employ eleven nuclear loci and the mitochondrial control region to investigate the phylogeography and historical demography of the pelagic seabird White‐faced Storm‐petrel (Pelagodroma marina) by sampling subspecies across its antitropical distribution. Groups are all highly differentiated: global mitochondrial Φ_ST = 0.89 (P < 0.01) and global nuclear Φ_ST varies between 0.22 and 0.83 (all P < 0.01). The complete lineage sorting of the mitochondrial locus between hemispheres is corroborated by approximately half of the nuclear genealogies, suggesting a long‐term antitropical divergence in isolation. Coalescent‐based estimates of demographic parameters suggest that hemispheric divergence of P. marina occurred approximately 840 000 ya (95% HPD 582 000–1 170 000), in the absence of gene flow, and divergence within the Southern Hemisphere occurred 190 000 ya (95% HPD 96 000–600 000), both probably associated with the profound palaeo‐oceanographic changes of the Pleistocene. A fledgling sampled in St Helena (tropical South Atlantic) suggests recent colonization from the Northern Hemisphere. Despite the great potential for long‐distance dispersal, P. marina antitropical groups have been evolving as independent, allopatric lineages, and divergence is probably maintained by philopatry coupled with asynchronous reproductive phenology and local adaptation.     

A comparison between data requirements and availability for calibrating predictive ecological models for lowland UK woodlands: learning new tricks from old trees

Woodlands provide valuable ecosystem services, and it is important to understand their dynamics. To predict the way in which these might change, we need process‐based predictive ecological models, but these are necessarily very data intensive. We tested the ability of existing datasets to provide the parameters necessary to instantiate a well‐used forest model (SORTIE) for a well‐studied woodland (Wytham Woods). Only five of SORTIE's 16 equations describing different aspects of the life history and behavior of individual trees could be parameterized without additional data collection. One age class – seedlings – was completely missed as they are shorter than the height at which Diameter at Breast Height (DBH) is measured. The mensuration of trees has changed little in the last 400 years (focussing almost exclusively on DBH) despite major changes in the nature of the source of value obtained from trees over this time. This results in there being insufficient data to parameterize process‐based models in order to meet the societal demand for ecological prediction. We do not advocate ceasing the measurement of DBH, but we do recommend that those concerned with tree mensuration consider whether additional measures of trees could be added to their data collection protocols. We also see advantages in integrating techniques such as ground‐based LIDAR or remote sensing techniques with long‐term datasets to both preserve continuity with what has been performed in the past and to expand the range of measurements made.     

Glycolate from microalgae: an efficient carbon source for biotechnological applications

Glycolate is produced in autotrophic cells under high temperatures and C_i‐limitation via oxygenation of ribulose‐1,5‐bisphosphate. In unicellular algae, glycolate is lost via excretion or metabolized via the C₂ cycle by consuming reductants, ATP and CO₂ emission (photorespiration). Therefore, photorespiration is an inhibitory process for biomass production. However, cells can be manipulated in a way that they become glycolate‐producing ‘cell factories’, when the ratio carboxylation/oxygenation is 2. If under these conditions the C₂ cycle is blocked, glycolate excretion becomes the only pathway of photosynthetic carbon flow. The study aims to proof the biotechnological applicability of algal‐based glycolate excretion as a new biotechnological platform. It is shown that cells of Chlamydomonas can be cultivated under specific conditions to establish a constant and long‐term stable glycolate excretion during the light phase. The cultures achieved a high efficiency of 82% of assimilated carbon transferred into glycolate biosynthesis without losses of function in cell vitality. Moreover, the glycolate accumulation in the medium is high enough to be directly used for microbial fermentation but does not show toxic effects to the glycolate‐producing cells.     

Speciation with gene flow: Evidence from a complex of alpine butterflies (Coenonympha,Satyridae)

Until complete reproductive isolation is achieved, the extent of differentiation between two diverging lineages is the result of a dynamic equilibrium between genetic isolation and mixing. This is especially true for hybrid taxa, for which the degree of isolation in regard to their parental species is decisive in their capacity to rise as a new and stable entity. In this work, we explored the past and current patterns of hybridization and divergence within a complex of closely related butterflies in the genus Coenonympha in which two alpine species, C. darwiniana and C. macromma, have been shown to result from hybridization between the also alpine C. gardetta and the lowland C. arcania. By testing alternative scenarios of divergence among species, we show that gene flow has been uninterrupted throughout the speciation process, although leading to different degrees of current genetic isolation between species in contact zones depending on the pair considered. Nonetheless, at broader geographic scale, analyses reveal a clear genetic differentiation between hybrid lineages and their parental species, pointing out to an advanced stage of the hybrid speciation process. Finally, the positive correlation observed between ecological divergence and genetic isolation among these butterflies suggests a potential role for ecological drivers during their speciation processes.     

Fatal toxoplasmosis in a southern muriqui (Brachyteles arachnoides) from São Paulo state,Brazil: Pathological,immunohistochemical, and molecular characterization

We report the pathological, immunohistochemical, and molecular features of fatal acute systemic toxoplasmosis in an adult, female, free‐living southern muriqui (Brachyteles arachnoides) from São Paulo state, Brazil. PCR‐RFLP genotyping analysis identified the #21 genotype of Toxoplasma gondii. This represents the first report of acute toxoplasmosis involving this genotype in humans and animals.     

Loci under selection during multiple range expansions of an invasive plant are mostly population specific,but patterns are associated with climate

Identifying the genes underlying rapid evolutionary changes, describing their function and ascertaining the environmental pressures that determine fitness are the central elements needed for understanding of evolutionary processes and phenotypic changes that improve the fitness of populations. It has been hypothesized that rapid adaptive changes in new environments may contribute to the rapid spread and success of invasive plants and animals. As yet, studies of adaptation during invasion are scarce, as is knowledge of the genes underlying adaptation, especially in multiple replicated invasions. Here, we quantified how genotype frequencies change during invasions, resulting in rapid evolution of naturalized populations. We used six fully replicated common garden experiments in Brazil where Pinus taeda (loblolly pine) was introduced at the same time, in the same numbers, from the same seed sources, and has formed naturalized populations expanding outward from the plantations. We used a combination of nonparametric, population genetics and multivariate statistics to detect changes in genotype frequencies along each of the six naturalization gradients and their association with climate as well as shifts in allele frequencies compared to the source populations. Results show 25 genes with significant shifts in genotype frequencies. Six genes had shifts in more than one population. Climate explained 25% of the variation in the groups of genes under selection across all locations, but specific genes under strong selection during invasions did not show climate‐related convergence. In conclusion, we detected rapid evolutionary changes during invasive range expansions, but the particular gene‐level patterns of evolution may be population specific.     

Leaf phenomics: a systematic reverse genetic screen for Arabidopsis leaf mutants

The study and eventual manipulation of leaf development in plants requires a thorough understanding of the genetic basis of leaf organogenesis. Forward genetic screens have identified hundreds of Arabidopsis mutants with altered leaf development, but the genome has not yet been saturated. To identify genes required for leaf development we are screening the Arabidopsis Salk Unimutant collection. We have identified 608 lines that exhibit a leaf phenotype with full penetrance and almost constant expressivity and 98 additional lines with segregating mutant phenotypes. To allow indexing and integration with other mutants, the mutant phenotypes were described using a custom leaf phenotype ontology. We found that the indexed mutation is present in the annotated locus for 78% of the 553 mutants genotyped, and that in half of these the annotated T‐DNA is responsible for the phenotype. To quickly map non‐annotated T‐DNA insertions, we developed a reliable, cost‐effective and easy method based on whole‐genome sequencing. To enable comprehensive access to our data, we implemented a public web application named PhenoLeaf ( http://genetics.umh.es/phenoleaf ) that allows researchers to query the results of our screen, including text and visual phenotype information. We demonstrated how this new resource can facilitate gene function discovery by identifying and characterizing At1g77600, which we found to be required for proximal–distal cell cycle‐driven leaf growth, and At3g62870, which encodes a ribosomal protein needed for cell proliferation and chloroplast function. This collection provides a valuable tool for the study of leaf development, characterization of biomass feedstocks and examination of other traits in this fundamental photosynthetic organ.     

Development of microsatellite markers for an extremely limited distributed rare diving beetle species,Acilius kishii,and a widely distributed species,Acilius japonicus (Coleoptera: Dytiscidae)

Acilius kishii Nakane, 1963 (Coleoptera: Dytiscidae) is an endangered diving beetle species distributed in only one location, Lake Yashaga‐Ike, Honshu Island, Japan. Acilius japonicus, which is related to A. kishii, is distributed widely in northern Honshu Island and Hokkaido Island in Japan. In this study, we identified 14 microsatellite loci for A. kishii and A. japonicus, including both polymorphic and monomorphic loci, using the next‐generation sequencing method. We observed that 5 and 10 loci showed polymorphisms in 31 and 32 individuals of A. kishii and A. japonicus, respectively. The observed and expected heterozygosities were 0.00–1.00 and 0.00–0.74, respectively. These microsatellite loci could be useful for future conservation genetic studies, including monitoring of genetic diversity and extinction risk of A. kishii.     

Identification and genetic diversity analysis of strain Pseudomonas syringae S5: A pathogen responsible for bacteriosis in Avena sativa plants

The genus Pseudomonas includes pathogenic species P. syringae, which can be found in various agricultural environments and which can affect a wide variety of plants, causing significant economic losses when the environmental conditions for its proliferation are optimal. Comprehensive characterizations of phytopathogenic bacteria belonging to the genus Pseudomonas are scarce in Argentina. In this work, the tabtoxin‐producing strain Pseudomonas S5, isolated from oat, was identi?ed as a P. syringae through biochemical tests such as the LOPAT test, and genetic tests such as the analysis of the small subunit ribosomal RNA gene (16S rRNA) sequence and repetitive elements, using BOX and ERIC primers. It was also determined that this phytopathogen is potentially capable of infecting other crops of agricultural importance for our region, such as soybean. This ability to infect different hosts gives it an adaptive advantage that allows it to endure seasonal changes in the environment where it lives. Our work contributes to the physiological classification of the phytopathogen P. syringae S5 isolated from our region, as well as to the knowledge about its range of potential hosts.     

First record of the bacterial endosymbiont Wolbachia for phytophagous hoverflies from genus Merodon (Diptera: Syrphidae)

Wolbachia is a widespread bacterial endosymbiont among arthropod species. It influences the reproduction of the host species and also mitochondrial DNA diversity. Until now there were only a few studies that detected Wolbachia infections in hoverflies (Diptera: Syrphidae), and this is the first broader study with the aim of examining the incidence of Wolbachia in the hoverfly genus Merodon. The obtained results indicate an infection rate of 96% and the presence of both Wolbachia supergroup A and B, which are characteristic for most of the infected arthropod species. Additionally, the presence of multiple Wolbachia strains in the Merodon aureus group species was detected and the mitochondrial DNA COI‐based relationships of the group are discussed in the light of infection. Finally, we discuss plant‐mediated horizontal transmission of Wolbachia strains among the studied hoverfly species.     

Modelling occupancy of an imperilled stream fish at multiple scales while accounting for imperfect detection: implications for conservation

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