Digital gene expression analysis of the zebra finch genome

Background: In order to understand patterns of adaptation and molecular evolution it is important to quantify both variation in gene expression and nucleotide sequence divergence. Gene expression profiling in non-model organisms has recently been facilitated by the advent of massively parallel sequencing technology. Here we investigate tissue specific gene expression patterns in the zebra finch (Taeniopygia guttata) with special emphasis on the genes of the major histocompatibility complex (MHC). Results: Almost 2 million 454-sequencing reads from cDNA of six different tissues were assembled and analysed. A total of 11,793 zebra finch transcripts were represented in this EST data, indicating a transcriptome coverage of about 65%. There was a positive correlation between the tissue specificity of gene expression and non-synonymous to synonymous nucleotide substitution ratio of genes, suggesting that genes with a specialised function are evolving at a higher rate (or with less constraint) than genes with a more general function. In line with this, there was also a negative correlation between overall expression levels and expression specificity of contigs. We found evidence for expression of 10 different genes related to the MHC. MHC genes showed relatively tissue specific expression levels and were in general primarily expressed in spleen. Several MHC genes, including MHC class I also showed expression in brain. Furthermore, for all genes with highest levels of expression in spleen there was an overrepresentation of several gene ontology terms related to immune function. Conclusions: Our study highlights the usefulness of next-generation sequence data for quantifying gene expression in the genome as a whole as well as in specific candidate genes. Overall, the data show predicted patterns of gene expression profiles and molecular evolution in the zebra finch genome. Expression of MHC genes in particular, corresponds well with expression patterns in other vertebrates

A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata)

Background: Genetic linkage maps are essential tools when searching for quantitative trait loci (QTL). To maximize genome coverage and provide an evenly spaced marker distribution a combination of different types of genetic marker are sometimes used. In this study we created linkage maps of four zebra finch (Taeniopygia guttata) chromosomes (1, 1A, 2 and 9) using two types of marker, Single Nucleotide Polymorphisms (SNPs) and microsatellites. To assess the effectiveness and accuracy of each kind of marker we compared maps built with each marker type separately and with both types of marker combined. Linkage map marker order was validated by making comparisons to the assembled zebra finch genome sequence. Results: We showed that marker order was less reliable and linkage map lengths were inflated for microsatellite maps relative to SNP maps, apparently due to differing error rates between the two types of marker. Guidelines on how to minimise the effects of error are provided. In particular, we show that when combining both types of marker the conventional process of building linkage maps, whereby the most informative markers are added to the map first, has to be modified in order to improve map accuracy. Conclusions: When using multiple types and large numbers of markers to create dense linkage maps, the least error prone loci (SNPs) rather than the most informative should be used to create framework maps before the addition of other potentially more error prone markers (microsatellites). This raises questions about the accuracy of marker order and predicted recombination rates in previous microsatellite linkage maps which were created using the conventional building process, however, provided suitable error detection strategies are followed microsatellite-based maps can continue to be regarded as reasonably reliable

Long sperm fertilize more eggs in a bird

Sperm competition, in which the ejaculates of multiple males compete to fertilize a female's ova, results in strong selection on sperm traits. Although sperm size and swimming velocity are known to independently affect fertilization success in certain species, exploring the relationship between sperm length, swimming velocity and fertilization success still remains a challenge. Here, we use the zebra finch (Taeniopygia guttata), where sperm size influences sperm swimming velocity, to determine the effect of sperm total length on fertilization success. Sperm competition experiments, in which pairs of males whose sperm differed only in length and swimming speed, revealed that males producing long sperm were more successful in terms of (i) the number of sperm reaching the ova and (ii) fertilizing those ova. Our results reveal that although sperm length is the main factor determining the outcome of sperm competition, complex interactions between male and female reproductive traits may also be important. The mechanisms underlying these interactions are poorly understood, but we suggest that differences in sperm storage and utilization by females may contribute to the outcome of sperm competition

Sperm morphology, adenosine triphosphate (ATP) concentration and swimming velocity: unexpected relationships in a passerine bird.

The relationship between sperm energetics and sperm function is poorly known, but is central to our understanding of the evolution of sperm traits. The aim of this study was to examine how sperm morphology and ATP content affect sperm swimming velocity in the zebra finch Taeniopygia guttata We exploited the high inter-male variation in this species and created extra experimental power by increasing the number of individuals with very long or short sperm through artificial selection. We found a pronounced quadratic relationship between total sperm length and swimming velocity, with velocity increasing with length up to a point, but declining in the very longest sperm. We also found an unexpected negative association between midpiece length and ATP content: sperm with a short midpiece generally contained the highest concentration of ATP. Low intracellular ATP is therefore unlikely to explain reduced swimming velocity among the very longest sperm (which tend to have a shorter midpiece)

ORAL RABIES VACCINATION: REDUCING ECONOMIC UNCERTAINTY VIA RESPONSE SURFACE ANALYSIS

Economic uncertainty surrounds the distribution of Raboral V-RG7 as an oral rabies vaccine (ORV) bait for the containment or elimination of raccoon-variant rabies in the United States. This paper describes a costs-savings model of ORV. It also describes Excel XP7 code that was prepared to compute potential net savings (NS) and benefit-cost ratios (BCRs) associated with Raboral V-RG7 bait distributions. Currently, baits and bait distributions are relatively expensive; individual baits are produced at a cost of $1.27 for federal use and typically dispensed at \u3e75 baits/km2. Distribution is estimated at$8.62/km2, $15.80/km2, and$33.30/km2 for fixed-winged (FW), ground (Gnd), and rotary-winged (RW) applications, respectively. Although many assumptions are required, iterative runs of the code allow plotting NS and BCR response surfaces for diverse scenarios based on 6 ORV variables: area (km2), bait-price (US/vaccine bait), bait-density (#/km2), application frequency (n), mode-of-delivery [US for % fixed-winged (FW), % rotarywinged (RW), and % ground-dispensed (Gnd)], and effectiveness (% seropositive titer conversion). Using a raccoon-rabies-epizootic-containment scenario for parts of Pennsylvania and a modest epizootic cost estimate of $40 million, the greatest NS ($6.4 to 38.4 million) and BCR (2.85 to 25.76) indices occurred for a one-time bait distribution involving FW aircraft over a fourth of the state with a $0.90/bait price. As expected, greater reliance on the more expensive RW and Gnd modes of bait distribution compared to FW aircraft, coupled with higher bait prices and higher bait densities, decreased NS and BCR indices. The utility of the approach to economic forecasting and decision making of ORV effects are discussed

Tactics and Economics of Wildlife Oral Rabies Vaccination, Canada and the United States

Progressive elimination of rabies in wildlife has been a general strategy in Canada and the United States; common campaign tactics are trap–vaccinate–release (TVR), point infection control (PIC), and oral rabies vaccination (ORV). TVR and PIC are labor intensive and the most expensive tactics per unit area (≈$616/km2 [in 2008 Can$, converted from the reported $450/km2 in 1991 Can$] and ≈$612/km2 [$500/km2 in 1999 Can$], respectively), but these tactics have proven crucial to elimination of raccoon rabies in Canada and to maintenance of ORV zones for preventing the spread of raccoon rabies in the United States. Economic assessments have shown that during rabies epizootics, costs of human post-exposure prophylaxis, pet vaccination, public health, and animal control spike. Modeling studies, involving diverse assumptions, have shown that ORV programs can be cost-efficient and yield benefit:cost ratios \u3e1.0

Linkage mapping reveals sex-dimorphic map distances in a passerine bird

Linkage maps are lacking for many highly influential model organisms in evolutionary research, including all passerine birds. Consequently, their full potential as research models is severely hampered. Here, we provide a partial linkage map and give novel estimates of sex-specific recombination rates in a passerine bird, the great reed warbler (Acrocephalus arundinaceus). Linkage analysis of genotypic data at 51 autosomal microsatellites and seven markers on the Z-chromosome (one of the sex chromosomes) from an extended pedigree resulted in 12 linkage groups with 2–8 loci. A striking feature of the map was the pronounced sex-dimorphism: males had a substantially lower recombination rate than females, which resulted in a suppressed autosomal map in males (sum of linkage groups: 110.2cM) compared to females (237.2cM; female/male map ratio: 2.15). The sex-specific recombination rates will facilitate the building of a denser linkage map and cast light on hypotheses about sex-specific recombination rates

Bada Bang, Bada Boom: Dispersal of fall migrating cormorants to protect sportfish on Oneida Lake, New York

The interior population of double-crested cormorants (Phalacrocorax auritus) continues to increase. As a result, conflicts between human interests and cormorants have intensified. The impacts of nesting, roosting, and migrating cormorants include predation at aquaculture facilities, interspecific competition with rare species including common terns {Sterna hirundo), and impacts to private property. In addition, heightened public and scientific debate regarding cormorant impacts on sportfish has accelerated the need for effective, socially acceptable methods for managing local conflicts. In 1998 and 1999, USDA, APHIS, Wildlife Services; the New York State Department of Environmental Conservation; and USGS, New York Fish and Wildlife Research Cooperative collaborated on a pilot project to investigate prospective methods and strategies for reducing predation of yellow perch (Perca flavescens) and walleye (Stizostedion vitreum) by fall migrating cormorants on Oneida Lake, New York. The goal of the cooperative program was to reduce stopover time, thereby reducing predation on fish stocks by migrating cormorants. A lakewide integrated non-lethal harassment and roost management program was initiated to disperse local and migrating cormorants from September to October each year. A variety of methods were used to manage cormorants including: electronic guards, propane cannons, mylar tape, human effigies, pyrotechnics, and dispersing birds with a boat. Harassment was focused on birds loafing on the water as well as day and night roosting sites (8 day and 2 night roosts). A total of 52,840 cormorants was dispersed (in many cases individual birds were harassed multiple times) using 1,518 pyrotechnics and 649 staff hours on the lake during the 2 years of the program. Surveys documented a 61%-98% reduction of the cormorants population on Oneida Lake compared to mean counts during the same time period from 1995-1997. Estimated total annual fish consumption by cormorants was reduced by 30% in 1998. Some off-site impacts of the program were seen with increased flocks of cormorants documented on nearby lakes

A prospective study of androgen levels, hormone-related genes and risk of rheumatoid arthritis

Introduction Rheumatoid arthritis (RA) is more common in females than males and sex steroid hormones may in part explain this difference. We conducted a case–control study nested within two prospective studies to determine the associations between plasma steroid hormones measured prior to RA onset and polymorphisms in the androgen receptor (AR), estrogen receptor 2 (ESR2), aromatase (CYP19) and progesterone receptor (PGR) genes and RA risk. Methods We genotyped AR, ESR2, CYP19, PGR SNPs and the AR CAG repeat in RA case–control studies nested within the Nurses\u27 Health Study (NHS), NHS II (449 RA cases, 449 controls) and the Women\u27s Health Study (72 cases, and 202 controls). All controls were matched on cohort, age, Caucasian race, menopausal status, and postmenopausal hormone use. We measured plasma dehydroepiandrosterone sulfate (DHEAS), testosterone, and sex hormone binding globulin in 132 pre-RA samples and 396 matched controls in the NHS cohorts. We used conditional logistic regression models adjusted for potential confounders to assess RA risk. Results Mean age of RA diagnosis was 55 years in both cohorts; 58% of cases were rheumatoid factor positive at diagnosis. There was no significant association between plasma DHEAS, total testosterone, or calculated free testosterone and risk of future RA. There was no association between individual variants or haplotypes in any of the genes and RA or seropositive RA, nor any association for the AR CAG repeat. Conclusions Steroid hormone levels measured at a single time point prior to RA onset were not associated with RA risk in this study. Our findings do not suggest that androgens or the AR, ESR2, PGR, and CYP19 genes are important to RA risk in women