Multiplex microsatellite PCR panels for the neotropical mangrove Rhizophora mangle: combining efforts towards a cost-effective and modifiable tool to better inform conservation and management

Better-informed mangrove conservation and management practices are needed as the ecosystem services provided by these intertidal forests continue to be threatened by increasing anthropogenic pressures and climate change. Multiple layers of knowledge are required to achieve this goal, including insights into population genetics of mangrove species. Understanding the importance of population-genetic insights to conservation, multiple research groups have developed microsatellite loci for the widespread, neotropical red mangrove, Rhizophora mangle. However, although a wealth of genetic markers exist, empirical research is limited in the number of these loci employed. Here, we designed two multiplex PCR panels that combine seven novel loci developed for this work and eight previously-developed loci from three research groups to generate 15-locus genotypes, more than twice the average number of loci used in previous research, in only two PCR. We demonstrated utility in R. mangle from four sites across ~2500 km near this species’ northern latitudinal limits, and that these multiplex panels were better able to delineate populations than data subsets with numbers of loci comparable to previous research. We focus our discussion on how this tool is a more-informative, efficient (both in terms of time and resources), and easily-modifiable alternative to address many pressing conservation and management issues, such as the generation of baseline genetic data for areas not yet studied, better defining management units, and monitoring genetic effects of restoration projects. We also provide a quick protocol that outlines each step in this procedure to facilitate the use of this tool by others

Estimating Bacterial diversity in scirtothrips dorsalis (thysanoptera: thripidae) Via Next generation sequencing

The last 2 decades have produced a better understanding of insect-microbial associations and yielded some important opportunities for insect control. However, most of our knowledge comes from model systems. Thrips (Thysanoptera: Thripidae) have been understudied despite their global importance as invasive species, plant pests and disease vectors. Using a culture and primer independent next-generation sequencing and metagenomics pipeline, we surveyed the bacteria of the globally important pest, Scirtothrips dorsalis Hood. The most abundant bacterial phyla identified were Actinobacteria and Proteobacteria and the most abundant genera were Propionibacterium, Stenotrophomonas, and Pseudomonas. A total of 189 genera of bacteria were identified. The absence of any vertically transferred symbiont taxa commonly found in insects is consistent with other studies suggesting that thrips primarilly acquire resident microbes from their environment. This does not preclude a possible beneficial/intimate association between S. dorsalis and the dominant taxa identified and future work should determine the nature of these associations

Perinatal asphyxia: current status and approaches towards neuroprotective strategies, with focus on sentinel proteins

Delivery is a stressful and risky event menacing the newborn. The mother-dependent respiration has to be replaced by autonomous pulmonary breathing immediately after delivery. If delayed, it may lead to deficient oxygen supply compromising survival and development of the central nervous system. Lack of oxygen availability gives rise to depletion of NAD+ tissue stores, decrease of ATP formation, weakening of the electron transport pump and anaerobic metabolism and acidosis, leading necessarily to death if oxygenation is not promptly re-established. Re-oxygenation triggers a cascade of compensatory biochemical events to restore function, which may be accompanied by improper homeostasis and oxidative stress. Consequences may be incomplete recovery, or excess reactions that worsen the biological outcome by disturbed metabolism and/or imbalance produced by over-expression of alternative metabolic pathways. Perinatal asphyxia has been associated with severe neurological and psychiatric sequelae with delayed clinical onset. No specific treatments have yet been established. In the clinical setting, after resuscitation of an infant with birth asphyxia, the emphasis is on supportive therapy. Several interventions have been proposed to attenuate secondary neuronal injuries elicited by asphyxia, including hypothermia. Although promising, the clinical efficacy of hypothermia has not been fully demonstrated. It is evident that new approaches are warranted. The purpose of this review is to discuss the concept of sentinel proteins as targets for neuroprotection. Several sentinel proteins have been described to protect the integrity of the genome (e.g. PARP-1; XRCC1; DNA ligase IIIα; DNA polymerase β, ERCC2, DNA-dependent protein kinases). They act by eliciting metabolic cascades leading to (i) activation of cell survival and neurotrophic pathways; (ii) early and delayed programmed cell death, and (iii) promotion of cell proliferation, differentiation, neuritogenesis and synaptogenesis. It is proposed that sentinel proteins can be used as markers for characterising long-term effects of perinatal asphyxia, and as targets for novel therapeutic development and innovative strategies for neonatal care

The <i>Scirtothrips dorsalis</i> Species Complex: Endemism and Invasion in a Global Pest

<div><p>Invasive arthropods pose unique management challenges in various environments, the first of which is correct identification. This apparently mundane task is particularly difficult if multiple species are morphologically indistinguishable but accurate identification can be determined with DNA barcoding provided an adequate reference set is available. <i>Scirtothrips dorsalis</i> is a highly polyphagous plant pest with a rapidly expanding global distribution and this species, as currently recognized, may be comprised of cryptic species. Here we report the development of a comprehensive DNA barcode library for <i>S</i>. <i>dorsalis</i> and seven nuclear markers via next-generation sequencing for identification use within the complex. We also report the delimitation of nine cryptic species and two morphologically distinguishable species comprising the <i>S</i>. <i>dorsalis</i> species complex using histogram analysis of DNA barcodes, Bayesian phylogenetics, and the multi-species coalescent. One member of the complex, here designated the South Asia 1 cryptic species, is highly invasive, polyphagous, and likely the species implicated in tospovirus transmission. Two other species, South Asia 2, and East Asia 1 are also highly polyphagous and appear to be at an earlier stage of global invasion. The remaining members of the complex are regionally endemic, varying in their pest status and degree of polyphagy. In addition to patterns of invasion and endemism, our results provide a framework both for identifying members of the complex based on their DNA barcode, and for future species delimiting efforts.</p></div

Nucleotide diversity (<i>π</i>) for 33 populations of 6 species within the <i>Scirtothrips dorsalis</i> species complex (Table A of S1 File).

<p>Numbered populations correspond to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0123747#pone.0123747.t004" target="_blank">Table 4</a>. Population 35 is <i>S</i>. <i>aff</i>. <i>dorsalis</i>.</p

Population genetics parameters and tests.

<p>-Abbreviations: n-sample size, %C-frequency of common invasive haplotype.</p><p>-Descriptive statistics: π-nucleotide diversity, HD-haplotype diversity, τ-the date of population growth in mutational time under the expansion model, rg-raggedness, F*-Fu&Li’s F*, D*-Fu&Li’s D*, D-Tajima’s D, Fs-Fu’s Fs.</p><p>-Statistical tests: ND-probability of non-differentiation (used to justify combining India, Israel, and select invasive populations as panmictic), E_D-test of demographic expansion p-value, E_S-test of spatial expansion p-value.</p><p>-Descriptive statistics could not be calculated for populations with HD = 0.</p><p>-Expansion tests were conducted for panmictic populations and populations where n>7.</p><p>-Significance is assessed under a two-tailed test for all test statistics and ND and a one-tailed test for E_D and E_S.</p><p>-Bold denotes significance favoring expansion while italics denote significance rejecting an expansion model.</p><p>¹Farris <i>et al</i>. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0123747#pone.0123747.ref012" target="_blank">12</a>];</p><p>²The invasive panmictic population includes all populations with a sample size >7 and a common invasive haplotype frequency >90%.</p><p>Population genetics parameters and tests.</p

Ranges of species within the <i>Scirtothrips dorsalis</i> complex.

<p>AU1- Australia 1, AU2- Australia 2, AU3- Australia 3, EA2- East Asia 2, EA3- East Asia 3, EA4- East Asia 4. Includes haplotypes detected in this study (white, Table A of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0123747#pone.0123747.s003" target="_blank">S1 File</a>) and mined from GenBank (yellow, Table B of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0123747#pone.0123747.s003" target="_blank">S1 File</a>). The earth global view used in this figure consists of MODIS satellite data for the NASA Blue Marble 2002 project. These images are freely available to educators, scientists, museums, and the public.</p

South Asia 1 cryptic species portion of the <i>Scirtothrips dorsalis</i> COI gene tree (75% consensus) showing multiple invasive maternal lineages now present in Israel (orange/yellow), Japan (green), and South Asia, East Asia, and North America (purple, blue, brown).

<p>Support subtending each node is the posterior clade frequency out of 100. * denotes frequency in >99.9% of trees. A single member of the South Asia 2 cryptic species roots the tree. Includes DNA sequences from this study (Table A of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0123747#pone.0123747.s003" target="_blank">S1 File</a>) and those mined from GenBank (Table B of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0123747#pone.0123747.s003" target="_blank">S1 File</a>).</p

Bayes factors favor partitioned over unpartitioned phylogenetic analyses.

<p>¹A Bayes factor of at least 10 is interpreted as significant favoring the more complex partitioned model after Kass & Raftery [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0123747#pone.0123747.ref070" target="_blank">70</a>].</p><p>Bayes factors favor partitioned over unpartitioned phylogenetic analyses.</p