Projected Loss of a Salamander Diversity Hotspot as a Consequence of Projected Global Climate Change

Background: Significant shifts in climate are considered a threat to plants and animals with significant physiological limitations and limited dispersal abilities. The southern Appalachian Mountains are a global hotspot for plethodontid salamander diversity. Plethodontids are lungless ectotherms, so their ecology is strongly governed by temperature and precipitation. Many plethodontid species in southern Appalachia exist in high elevation habitats that may be at or near their thermal maxima, and may also have limited dispersal abilities across warmer valley bottoms. Methodology/Principal Findings: We used a maximum-entropy approach (program Maxent) to model the suitable climatic habitat of 41 plethodontid salamander species inhabiting the Appalachian Highlands region (33 individual species and eight species included within two species complexes). We evaluated the relative change in suitable climatic habitat for these species in the Appalachian Highlands from the current climate to the years 2020, 2050, and 2080, using both the HADCM3 and the CGCM3 models, each under low and high CO 2 scenarios, and using two-model thresholds levels (relative suitability thresholds for determining suitable/unsuitable range), for a total of 8 scenarios per species. Conclusion/Significance: While models differed slightly, every scenario projected significant declines in suitable habitat within the Appalachian Highlands as early as 2020. Species with more southern ranges and with smaller ranges had larger projected habitat loss. Despite significant differences in projected precipitation changes to the region, projections did no

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences

Detection and characterization of small insertion and deletion genetic variants in modern layer chicken genomes

Background: Small insertions and deletions (InDels) constitute the second most abundant class of genetic variants and have been found to be associated with many traits and diseases. The present study reports on the detection and characterisation of about 883 K high quality InDels from the whole-genome analysis of several modern layer chicken lines from diverse breeds. Results: To reduce the error rates seen in InDel detection, this study used the consensus set from two InDel-calling packages: SAMtools and Dindel, as well as stringent post-filtering criteria. By analysing sequence data from 163 chickens from 11 commercial and 5 experimental layer lines, this study detected about 883 K high quality consensus InDels with 93 % validation rate and an average density of 0.78 InDels/kb over the genome. Certain chromosomes, viz, GGAZ, 16, 22 and 25 showed very low densities of InDels whereas the highest rate was observed on GGA6. In spite of the higher recombination rates on microchromosomes, the InDel density on these chromosomes was generally lower relative to macrochromosomes possibly due to their higher gene density. About 43-87 % of the InDels were found to be fixed within each line. The majority of detected InDels (86 %) were 1-5 bases and about 63 % were non-repetitive in nature while the rest were tandem repeats of various motif types. Functional annotation identified 613 frameshift, 465 non-frameshift and 10 stop-gain/loss InDels. Apart from the frameshift and stopgain/loss InDels that are expected to affect the translation of protein sequences and their biological activity, 33 % of the non-frameshift were predicted as evolutionary intolerant with potential impact on protein functions. Moreover, about 2.5 % of the InDels coincided with the most-conserved elements previously mapped on the chicken genome and are likely to define functional elements. InDels potentially affecting protein function were found to be enriched for certain gene-classes e.g. those associated with cell proliferation, chromosome and Golgi organization, spermatogenesis, and muscle contraction. Conclusions: The large catalogue of InDels presented in this study along with their associated information such as functional annotation, estimated allele frequency, etc. are expected to serve as a rich resource for application in future research and breeding in the chicken

Uncertainty in continental-scale temperature predictions

Anthropogenic climate change has been detected on continental-scale regions on all inhabited continents of the World. From knowledge of the relative contributions of greenhouse gases and other forcings to observed temperature change it is possible to infer the likely rates of future warming, consistent with past observed temperature changes. Probabilistic forecasts of future warming rates in six continental-scale regions have been calculated by assuming that there is a linear relationship between past and future fractional error in temperature change on these spatial scales. All regions are expected to warm over the next century with the largest uncertainty in future warming rates being in North America and Europe. More tightly constrained predictions are obtained if it is assumed that fractional errors in global mean temperature change scale the regional projections. Copyright 2006 by the American Geophysical Union

Estimates of uncertainty in predictions of global mean surface temperature

A method for estimating uncertainty in future climate change is discussed in detail and applied to pridictions of global mean temperature change. The method uses optimal fingerprinting to make estimates of uncertainty in model simulations of twentieth-century warming. These estimates are then projected forward in time using a linear, compact relationship between twentieth-century warming and twenty-first-century warming. This relationship is established from a large ensemble of energy balance models. By varying the energy balance model parameters an estimate is made of the error associated with using the linear relationship in forecasts of twentieth-century global mean temperature. Including this error has very little impact on the forecasts. There is a 50% chance that the global mean temperature change between 1995 and 2035 will be greater than 1.5 K for the Special Report on Emissions Scenarios (SRES) A1FI scenario. Under SRES B2 the same threshold is not exceeded until 2055. These results should be relatively robust to model developments for a given radiative forcing history. © 2007 American Meteorological Society

Ribosome display of combinatorial antibody libraries derived from mice immunised with heat-killed Xylella fastidiosa and the selection of MopB-specific single-chain antibodies

Pierce's disease is a devastating lethal disease of Vitus vinifera grapevines caused by the bacterium Xylella fastidiosa. There is no cure for Pierce's disease and control is achieved predominantly by suppressing transmission of the glassy winged sharpshooter insect vector. We present a simple robust approach for the generation of panels of recombinant single chain antibodies against the surface exposed elements of X. fastidiosa that may have potential use in diagnosis and/or disease transmission blocking studies. In vitro combinatorial antibody ribosome display libraries were assembled from immunoglobulin transcripts rescued from the spleens of mice immunized with heat-killed X. fastidiosa. The libraries were used in a single round of selection against an outer-membrane protein MopB, resulting in the isolation of a panel of recombinant antibodies. The potential use of selected anti-MopB antibodies was demonstrated by the successful application of the 4XfMopB3 antibody in an ELISA, western blot and immunofluorescence assay. These immortalised in vitro recombinant single chain antibody libraries generated against heat killed X. fastidiosa are a resource for the Pierce's disease research community that may be readily accessed for the isolation of antibodies against a plethora of X. fastidiosa surface exposed antigenic molecules