Phylogeographic reconstruction of the marbled crayfish origin

The marbled crayfish (Procambarus virginalis) is a triploid and parthenogenetic freshwater crayfish species that has colonized diverse habitats around the world. Previous studies suggested that the clonal marbled crayfish population descended as recently as 25 years ago from a single specimen of P. fallax, the sexually reproducing parent species. However, the genetic, phylogeographic, and mechanistic origins of the species have remained enigmatic. We have now constructed a new genome assembly for P. virginalis to support a detailed phylogeographic analysis of the diploid parent species, Procambarus fallax. Our results strongly suggest that both parental haplotypes of P. virginalis were inherited from the Everglades subpopulation of P. fallax. Comprehensive whole-genome sequencing also detected triploid specimens in the same subpopulation, which either represent evolutionarily important intermediate genotypes or independent parthenogenetic lineages arising among the sexual parent population. Our findings thus clarify the geographic origin of the marbled crayfish and identify potential mechanisms of parthenogenetic speciation

Annulus Amplitudes and ZZ Branes in Minimal String Theory

We study the annulus amplitudes of (p,q) minimal string theory. Focusing on the ZZ-FZZT annulus amplitude as a target-space probe of the ZZ brane, we use it to confirm that the ZZ branes are localized in the strong-coupling region. Along the way we learn that the ZZ-FZZT open strings are fermions, even though our theory is bosonic! We also provide a geometrical interpretation of the annulus amplitudes in terms of the Riemann surface M_{p,q} that emerges from the FZZT branes. The ZZ-FZZT annulus amplitude measures the deformation of M_{p,q} due to the presence of background ZZ branes; each kind of ZZ-brane deforms only one A-period of the surface. Finally, we use the annulus amplitudes to argue that the ZZ branes can be regarded as "wrong-branch" tachyons which violate the bound \alpha<Q/2.Comment: 33 pages, new results in appendix, minor change

Branes, Rings and Matrix Models in Minimal (Super)string Theory

We study both bosonic and supersymmetric (p,q) minimal models coupled to Liouville theory using the ground ring and the various branes of the theory. From the FZZT brane partition function, there emerges a unified, geometric description of all these theories in terms of an auxiliary Riemann surface M_{p,q} and the corresponding matrix model. In terms of this geometric description, both the FZZT and ZZ branes correspond to line integrals of a certain one-form on M_{p,q}. Moreover, we argue that there are a finite number of distinct (m,n) ZZ branes, and we show that these ZZ branes are located at the singularities of M_{p,q}. Finally, we discuss the possibility that the bosonic and supersymmetric theories with (p,q) odd and relatively prime are identical, as is suggested by the unified treatment of these models.Comment: 72 pages, 3 figures, improved treatment of FZZT and ZZ branes, minor change

The maternal and early embryonic transcriptome of the milkweed bug Oncopeltus fasciatus

<p>Abstract</p> <p>Background</p> <p>Most evolutionary developmental biology ("evo-devo") studies of emerging model organisms focus on small numbers of candidate genes cloned individually using degenerate PCR. However, newly available sequencing technologies such as 454 pyrosequencing have recently begun to allow for massive gene discovery in animals without sequenced genomes. Within insects, although large volumes of sequence data are available for holometabolous insects, developmental studies of basally branching hemimetabolous insects typically suffer from low rates of gene discovery.</p> <p>Results</p> <p>We used 454 pyrosequencing to sequence over 500 million bases of cDNA from the ovaries and embryos of the milkweed bug <it>Oncopeltus fasciatus</it>, which lacks a sequenced genome. This indirectly developing insect occupies an important phylogenetic position, branching basal to Diptera (including fruit flies) and Hymenoptera (including honeybees), and is an experimentally tractable model for short-germ development. 2,087,410 reads from both normalized and non-normalized cDNA assembled into 21,097 sequences (isotigs) and 112,531 singletons. The assembled sequences fell into 16,617 unique gene models, and included predictions of splicing isoforms, which we examined experimentally. Discovery of new genes plateaued after assembly of ~1.5 million reads, suggesting that we have sequenced nearly all transcripts present in the cDNA sampled. Many transcripts have been assembled at close to full length, and there is a net gain of sequence data for over half of the pre-existing <it>O. fasciatus </it>accessions for developmental genes in GenBank. We identified 10,775 unique genes, including members of all major conserved metazoan signaling pathways and genes involved in several major categories of early developmental processes. We also specifically address the effects of cDNA normalization on gene discovery in <it>de novo </it>transcriptome analyses.</p> <p>Conclusions</p> <p>Our sequencing, assembly and annotation framework provide a simple and effective way to achieve high-throughput gene discovery for organisms lacking a sequenced genome. These data will have applications to the study of the evolution of arthropod genes and genetic pathways, and to the wider evolution, development and genomics communities working with emerging model organisms.</p> <p>[The sequence data from this study have been submitted to GenBank under study accession number SRP002610 (<url>http://www.ncbi.nlm.nih.gov/sra?term=SRP002610</url>). Custom scripts generated are available at <url>http://www.extavourlab.com/protocols/index.html</url>. Seven Additional files are available.]</p

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

Crayfish assemblage shifts in a large drought-prone wetland: the roles of hydrology and competition

1. Faster growing, larger and/or more aggressive crayfish species are predicted to dominate permanent waterbodies. We tested this prediction using a 9 year dataset for two species of crayfish (Procambarus alleni and Procambarus fallax) co-existing in a sub-tropical flowing slough in southern Florida. Using a series of laboratory and mesocosm experiments we also compared life history traits and performance of the respective species to test mechanisms that could explain dominance shifts in the local crayfish assemblages. 2. Over the 9-year period, P. alleni densities were the greatest in shallower, shorterhydroperiod areas bordering the slough, while P. fallax densities were higher in deeper, longer-hydroperiod central areas. These areas were separated by 0.8–2 km of continuous wetland with no apparent barriers to movement between them. 3. Density of P. fallax was not strongly affected by any measures of hydrological variation, while P. alleni density increased with more severe drought conditions. Following the strongest droughts, P. alleni colonized areas in the centre of the slough where they had been absent or scarce in wetter years. 4. We conducted experiments to compare growth rates, drought tolerance, and competitive dominance of these species. P. alleni survived drought conditions better, had higher growth rates, and was the dominant competitor for space and food. While drought probably limits P. fallax in the drier slough habitats, neither drought sensitivity nor interspecific competition with P. fallax can explain decreases of P. alleni with wetter conditions. 5. Our results indicate that a competition-colonization tradeoff cannot explain the crayfish compositional dynamics in this wetland because P. alleni is both the best competitor and the best at surviving in and colonizing areas with the strongest droughts. Future attention should focus on the potential for selective effects of predators that co-vary with hydrology. 6. The traits (large size, fast growth, competitive dominance) exhibited by P. alleni, which is absent in long-hydroperiod wetlands, are those exhibited by dominant crayfish in permanent lakes and streams containing fish. Although these traits make crayfish less vulnerable to fish in some lakes and streams, life-history models of community structure across permanence gradients suggest the opposite traits should be favoured for co-existence with fish

Estimation of Crayfish Abundance and Size-Structure in Diets of White Ibis Chicks

We investigated the use of crayfish gastroliths and exoskeleton pieces for quantifying crayfish abundance and size-structure in diets of White Ibis (Eudocimus albus) chicks in the Everglades. We then quantified cray fish and fish abundance from various small hard parts and intact fish heads in 23 boluses, taken from two nesting colonies in Water Conservation Area 3 (WCA 3) and Arthur R. Marshall Loxahatchee National Wildlife Refuge (Lox) in the Florida Everglades during May 2006. We determined that using gastroliths to estimate crayfish numbers in boluses had significant drawbacks; only a small fraction of field-caught crayfish bear gastroliths and the two crayfish species in the Everglades differ in percentage bearing gastroliths. In contrast, counts of crayfish rostrums and chelae pairs gave simple and similar estimates of crayfish in the boluses. The two colonies had strikingly different diets in May 2006; New Colony 3 (Lox) boluses were dominated by crayfish while birds from the Alley North (WCA 3) boluses were fish-dominated and had few crayfish. Using measurements of the crayfish rostrums we deter mined the size-structure of crayfish found in the diets of the New Colony 3 birds, and determined that the crayfish in the diet were relatively large (mean = 19 mm carapace length) when compared to the available crayfish in the marsh. These crayfish were also large relative to previous reports of crayfish found in White Ibis diets in the Everglades