Multiplexed microsatellite recovery using massively parallel sequencing.

Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of massively parallel sequencing (MPS), it is now possible to sequence microsatellite-enriched genomic libraries in multiplex pools. To test this approach, we prepared seven microsatellite-enriched, barcoded genomic libraries from diverse taxa (two conifer trees, five birds) and sequenced these on one lane of the Illumina Genome Analyzer using paired-end 80-bp reads. In this experiment, we screened 6.1 million sequences and identified 356,958 unique microreads that contained di- or trinucleotide microsatellites. Examination of four species shows that our conversion rate from raw sequences to polymorphic markers compares favourably to Sanger- and 454-based methods. The advantage of multiplexed MPS is that the staggering capacity of modern microread sequencing is spread across many libraries; this reduces sample preparation and sequencing costs to less than $400 (USD) per species. This price is sufficiently low that microsatellite libraries could be prepared and sequenced for all 1373 organisms listed as 'threatened' and 'endangered' in the United States for under $0.5 M (USD).

Elbow extension test to rule out elbow fracture: multicentre, prospective validation and observational study of diagnostic accuracy in adults and children.

OBJECTIVE: To determine whether full elbow extension as assessed by the elbow extension test can be used in routine clinical practice to rule out bony injury in patients presenting with elbow injury. DESIGN: Adults: multicentre prospective interventional validation study in secondary care. Children: multicentre prospective observational study in secondary care. SETTING: Five emergency departments in southwest England. PARTICIPANTS: 2127 adults and children presenting to the emergency department with acute elbow injury. INTERVENTION: Elbow extension test during routine care by clinical staff to determine the need for radiography in adults and to guide follow-up in children. MAIN OUTCOME MEASURES: Presence of elbow fracture on radiograph, or recovery with no indication for further review at 7-10 days. RESULTS: Of 1740 eligible participants, 602 patients were able to fully extend their elbow; 17 of these patients had a fracture. Two adult patients with olecranon fractures needed a change in treatment. In the 1138 patients without full elbow extension, 521 fractures were identified. Overall, the test had sensitivity and specificity (95% confidence interval) for detecting elbow fracture of 96.8% (95.0 to 98.2) and 48.5% (45.6 to 51.4). Full elbow extension had a negative predictive value for fracture of 98.4% (96.3 to 99.5) in adults and 95.8% (92.6 to 97.8) in children. Negative likelihood ratios were 0.03 (0.01 to 0.08) in adults and 0.11 (0.06 to 0.19) in children. CONCLUSION: The elbow extension test can be used in routine practice to inform clinical decision making. Patients who cannot fully extend their elbow after injury should be referred for radiography, as they have a nearly 50% chance of fracture. For those able to fully extend their elbow, radiography can be deferred if the practitioner is confident that an olecranon fracture is not present. Patients who do not undergo radiography should return if symptoms have not resolved within 7-10 days.

Parentage and relatedness in polyandrous comb-crested jacanas using ISSRs.

In this article we present the first analysis of parentage and relatedness in a natural vertebrate population, using Intersimple Sequence Repeat (ISSR) markers. Thus, 28 ISSR markers were used in a study of a sex-role reversed, simultaneously polyandrous shorebird from northeastern Australia, the comb-crested jacana (Irediparra gallinacea). Assessment of parentage was based on comparison of field observations, novel bands, individual-specific bands found in 7/9 males and 4/6 females, and a 99% CI exclusion criteria. Integrating results from these approaches resulted in confirmation of paternity in all 36 chicks. In only one case (2.8% of chicks) was a co-mate assigned paternity. Thus, comb-crested jacanas appear to be genetically monogamous. These results showed resemblance to sequentially polyandrous birds but differed from the simultaneously polyandrous wattled jacana ( Jacana jacana; Emlen et al. 1998). A significant relationship between relatedness and ISSR similarity resulted in recognition that 14/15 adults sampled may be related to at least one other adult by 0.25 or more. Lack of dispersal may be explained by physical limitations and adequate regional habitat. ISSRs proved to be simple and helpful in resolving these issues.

Population differentiation in randomly amplified polymorphic DNA of red-cockaded woodpeckers Picoides borealis.

Random amplified polymorphic DNA (RAPD) phenotypes generated by 13 primers were scored for 101 individuals in 14 populations of the endangered red-cockaded woodpecker Picoides borealis. Although no population-specific markers were found, the frequencies of several markers differed significantly among populations. Application of the recently developed AMOVA method (analysis of molecular variance; Excoffier, Smouse & Quattro 1992) showed that more than 90% of phenotypic variance occurred among individuals within populations; of the remaining variance, half was attributed among groups of geographically adjacent populations and half among populations within those groups. The statistical significance of these patterns was supported by Monte Carolo sampling simulations and permutation tests. Estimation of allele frequencies from phenotypes provided somewhat weaker evidence for population structure, although among-population variance in allele frequencies was detectable (Fst = 0.19; chi 2(169) = 509.3, P < 0.0001). UPGMA cluster analyses based on Rogers' (1972) genetic distance revealed grouping of some geographically proximate populations. A Mantel test indicated a positive (r = 0.16), although not significant, correlation between geographic and genetic distances. We compared a subset of our RAPD data with data from a previous study that used allozymes (Stangel, Lennartz & Smith 1992). RAPD (n = 75) and allozyme (n = 245) results based on samples from the same ten populations showed similar patterns. Our study indicates that RAPDs can be helpful in differentiating populations at the phenotypic level even when small sample sizes, estimation bias, and inability to test for Hardy-Weinberg equilibrium complicate the genotypic interpretation. Lack of large differences among populations of red-cockaded woodpeckers may allow flexibility in interpopulation translocations, provided factors such as habitat preference, latitudinal direction of translocation, and status of donor populations are considered.