Microsatellites for the marsh fritillary butterfly: de novo transcriptome sequencing, and a comparison with amplified fragment length polymorphism (AFLP) markers.

Journal ArticleResearch Support, Non-U.S. Gov'tBACKGROUND: Until recently the isolation of microsatellite markers from Lepidoptera has proved troublesome, expensive and time-consuming. Following on from a previous study of Edith's checkerspot butterfly, Euphydryas editha, we developed novel microsatellite markers for the vulnerable marsh fritillary butterfly, E. aurinia. Our goal was to optimize the process in order to reduce both time and cost relative to prevailing techniques. This was accomplished by using a combination of previously developed techniques: in silico mining of a de novo assembled transcriptome sequence, and genotyping the microsatellites found there using an economic method of fluorescently labelling primers. PRINCIPAL FINDINGS: In total, we screened nine polymorphic microsatellite markers, two of which were previously published, and seven that were isolated de novo. These markers were able to amplify across geographically isolated populations throughout Continental Europe and the UK. Significant deviations from Hardy-Weinberg equilibrium were evident in some populations, most likely due to the presence of null alleles. However, we used an F(st) outlier approach to show that these markers are likely selectively neutral. Furthermore, using a set of 128 individuals from 11 populations, we demonstrate consistency in population differentiation estimates with previously developed amplified fragment length polymorphism (AFLP) markers (r = 0.68, p<0.001). SIGNIFICANCE: Rapid development of microsatellite markers for difficult taxa such as Lepidoptera, and concordant results with other putatively neutral molecular markers, demonstrate the potential of de novo transcriptional sequencing for future studies of population structure and gene flow that are desperately needed for declining species across fragmented landscapes.BBSRCOkinawa Institute for Science and Technology (OIST

Coherent Neutrino Interactions in a Dense Medium

Motivated by the effect of matter on neutrino oscillations (the MSW effect) we study in more detail the propagation of neutrinos in a dense medium. The dispersion relation for massive neutrinos in a medium is known to have a minimum at nonzero momentum p \sim (G_F\rho)/\sqrt{2}. We study in detail the origin and consequences of this dispersion relation for both Dirac and Majorana neutrinos both in a toy model with only neutral currents and a single neutrino flavour and in a realistic "Standard Model" with two neutrino flavours. We find that for a range of neutrino momenta near the minimum of the dispersion relation, Dirac neutrinos are trapped by their coherent interactions with the medium. This effect does not lead to the trapping of Majorana neutrinos.Comment: 28 pages, 6 figures, Latex; minor changes, one reference added; version to appear in Phys. Rev.

Natural History of the Slave Making Ant, Polyergus lucidus, Sensu lato in Northern Florida and Its Three Formica pallidefulva Group Hosts

Slave making ants of the Polyergus lucidus Mayr (Hymenoptera: Formicidae) complex enslave 3 different Formica species, Formica archboldi, F. dolosa, and F. pallidefalva, in northern Florida. This is the first record of presumed P. lucidus subspecies co-occurring with and enslaving multiple Formica hosts in the southern end of their range. The behavior, colony sizes, body sizes, nest architecture, and other natural history observations of Polyergus colonies and their Formica hosts are reported. The taxonomic and conservation implications of these observations are discussed

Neutrino ground state in a dense star

It has recently been argued that long range forces due to the exchange of massless neutrinos give rise to a very large self-energy in a dense, finite-ranged, weakly-charged medium. Such an effect, if real, would destabilize a neutron star. To address this issue we have studied the related problem of a massless neutrino field in the presence of an external, static electroweak potential of finite range. To be precise, we have computed to one loop the exact vacuum energy for the case of a spherical square well potential of depth alpha and radius R. For small wells, the vacuum energy is reliably determined by a perturbative expansion in the external potential. For large wells, however, the perturbative expansion breaks down. A manifestation of this breakdown is that the vacuum carries a non-zero neutrino charge. The energy and neutrino charge of the ground state are, to a good approximation for large wells, those of a neutrino condensate with chemical potential mu=alpha. Our results demonstrate explicitly that long-range forces due to the exchange of massless neutrinos do not threaten the stability of neutron stars.Comment: 27 pages, 7 figures, revtex; several typos corrected; a few references added; title changed slightly; includes a "note added in proof"; version to appear in Phys. Rev.

Monoculture of Leafcutter Ant Gardens

Background -- Leafcutter ants depend on the cultivation of symbiotic Attamyces fungi for food, which are thought to be grown by the ants in single-strain, clonal monoculture throughout the hundreds to thousands of gardens within a leafcutter nest. Monoculture eliminates cultivar-cultivar competition that would select for competitive fungal traits that are detrimental to the ants, whereas polyculture of several fungi could increase nutritional diversity and disease resistance of genetically variable gardens. Methodology/Principal Findings -- Using three experimental approaches, we assessed cultivar diversity within nests of Atta leafcutter ants, which are most likely among all fungus-growing ants to cultivate distinct cultivar genotypes per nest because of the nests' enormous sizes (up to 5000 gardens) and extended lifespans (10–20 years). In Atta texana and in A. cephalotes, we resampled nests over a 5-year period to test for persistence of resident cultivar genotypes within each nest, and we tested for genetic differences between fungi from different nest sectors accessed through excavation. In A. texana, we also determined the number of Attamyces cells carried as a starter inoculum by a dispersing queens (minimally several thousand Attamyces cells), and we tested for genetic differences between Attamyces carried by sister queens dispersing from the same nest. Except for mutational variation arising during clonal Attamyces propagation, DNA fingerprinting revealed no evidence for fungal polyculture and no genotype turnover during the 5-year surveys. Conclusions/Significance -- Atta leafcutter ants can achieve stable, fungal monoculture over many years. Mutational variation emerging within an Attamyces monoculture could provide genetic diversity for symbiont choice (gardening biases of the ants favoring specific mutational variants), an analog of artificial selection.The research was supported by National Science Foundation awards DEB-0920138, DEB-0639879, and DEB-0110073 to UGM; DEB-0949689 to T.R. Schultz, N. Mehdiabadi, and UGM; and a Fellowship (02/05) from the Conselho Nacional de Desenvolvimento Científico e Tecnológico to AR. The funding agencies had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Biological Sciences, School o

Microsatellite discovery in an insular amphibian (Grandisonia alternans) with comments on cross-species utility and the accuracy of locus identification from unassembled Illumina data

The Seychelles archipelago is unique among isolated oceanic islands because it features an endemic radiation of caecilian amphibians (Gymnophiona). In order to develop population genetics resources for this system, we identified microsatellite loci using unassembled Illumina MiSeq data generated from a genomic library of Grandisonia alternans, a species that occurs on multiple islands in the archipelago. Applying a recently described method (PALFINDER) we identified 8001 microsatellite loci that were potentially informative for population genetics analyses. Of these markers, we screened 60 loci using five individuals, directly sequenced several amplicons to confirm their identity, and then used eight loci to score allele sizes in 64 G. alternans individuals originating from five islands. A number of these individuals were sampled using non-lethal methods, demonstrating the efficacy of non-destructive molecular sampling in amphibian research. Although two loci satisfied our criteria as diploid, neutrally evolving loci with the statistical power to detect population structure, our success in identifying reliable loci was very low. Additionally, we discovered some issues with primer redundancy and differences between Illumina and Sanger sequences that suggest some Illumina-inferred loci are invalid. We investigated cross-species utility for eight loci and found most could be successfully amplified, sequenced and aligned across other species and genera of caecilians from the Seychelles. Thus, our study in part supported the validity of using PALFINDER with unassembled reads for microsatellite discovery within and across species, but importantly identified major limitations to applying this approach to small datasets (ca. 1 million reads) and loci with small tandem repeat sizes

Ethological principles predict the neuropeptides co-opted to influence parenting

Ethologists predicted that parental care evolves by modifying behavioural precursors in the asocial ancestor. As a corollary, we predict that the evolved mechanistic changes reside in genetic pathways underlying these traits. Here we test our hypothesis in female burying beetles, Nicrophorus vespilloides, an insect where caring adults regurgitate food to begging, dependent offspring. We quantify neuropeptide abundance in brains collected from three behavioural states: solitary virgins, individuals actively parenting or post-parenting solitary adults and quantify 133 peptides belonging to 18 neuropeptides. Eight neuropeptides differ in abundance in one or more states, with increased abundance during parenting in seven. None of these eight neuropeptides have been associated with parental care previously, but all have roles in predicted behavioural precursors for parenting. Our study supports the hypothesis that predictable traits and pathways are targets of selection during the evolution of parenting and suggests additional candidate neuropeptides to study in the context of parenting

Degenerate and Other Neutrino Mass Scenarios and Dark Matter

I discuss in this talk mainly three topics related with dark matter motivated neutrino mass spectrum and a generic issue of mass pattern, the normal versus the inverted mass hierarchies. In the first part, by describing failure of a nontrivial potential counter example, I argue that the standard 3 $\nu$ mixing scheme with the solar and the atmospheric $\Delta m^2$'s is robust. In the second part, I discuss the almost degenerate neutrino (ADN) scenario as the unique possibility of accommodating dark matter mass neutrinos into the 3 $\nu$ scheme. I review a cosmological bound and then reanalyze the constraints imposed on the ADN scenario with the new data of double beta decay experiment. In the last part, I discuss the 3 $\nu$ flavor transformation in supernova (SN) and point out the possibility that neutrinos from SN may distinguish the normal versus inverted hierarchies of neutrino masses. By analyzing the neutrino data from SN1987A, I argue that the inverted mass hierarchy is disfavored by the data

Microbiomes of ant castes implicate new microbial roles in the fungus-growing ant Trachymyrmex septentrionalis

Fungus-growing ants employ several defenses against diseases, including disease-suppressing microbial biofilms on their integument and in fungal gardens. Here, we compare the phenology of microbiomes in natural nests of the temperate fungus-growing ant Trachymyrmex septentrionalis using culture-dependent isolations and culture-independent 16S-amplicon 454-sequencing. 454-sequencing revealed diverse actinobacteria associated with ants, including most prominently Solirubrobacter (12.2–30.9% of sequence reads), Pseudonocardia (3.5–42.0%), and Microlunatus (0.4–10.8%). Bacterial abundances remained relatively constant in monthly surveys throughout the annual active period (late winter to late summer), except Pseudonocardia abundance declined in females during the reproductive phase. Pseudonocardia species found on ants are phylogenetically different from those in gardens and soil, indicating ecological separation of these Pseudonocardia types. Because the pathogen Escovopsis is not known to infect gardens of T. septentrionalis, the ant-associated microbes do not seem to function in Escovopsis suppression, but could protect against ant diseases, help in nest sanitation, or serve unknown functions