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Identification of microsatellites, or simple sequence repeats (SSRs), can be a time-consuming and costly investment requiring enrichment, cloning, and sequencing of candidate loci. Recently, however, high throughput sequencing (with or without prior enrichment for specific SSR loci) has been utilized to identify SSR loci. The direct “Seq-to-SSR” approach has an advantage over enrichment-based strategies in that it does not require a priori selection of particular motifs, or prior knowledge of genomic SSR content. It has been more expensive per SSR locus recovered, however, particularly for genomes with few SSR loci, such as bird genomes. The longer but relatively more expensive 454 reads have been preferred over less expensive Illumina reads. Here, we use Illumina paired-end sequence data to identify potentially amplifiable SSR loci (PALs) from a snake (the Burmese python, Python molurus bivittatus), and directly compare these results to those from 454 data. We also compare the python results to results from Illumina sequencing of two bird genomes (Gunnison Sage-grouse, Centrocercus minimus, and Clark's Nutcracker, Nucifraga columbiana), which have considerably fewer SSRs than the python. We show that direct Illumina Seq-to-SSR can identify and characterize thousands of potentially amplifiable SSR loci for as little as $10 per sample – a fraction of the cost of 454 sequencing. Given that Illumina Seq-to-SSR is effective, inexpensive, and reliable even for species such as birds that have few SSR loci, it seems that there are now few situations for which prior hybridization is justifiable.

Eight white pine species are widely distributed among the forests of western Canada and the United States. The different forest communities with these species contribute biodiversity to the western landscape. The trees themselves provide various ecosystem services, including wildlife habitat and watershed protection. White pine communities range in elevation from lower to upper treeline, in successional stage from seral to climax, and in stand type from krummholz to closed-canopy forest. Many white pine species are moderately to strongly fire-dependent for regeneration; several species are extreme stress tolerators and persistent on harsh sites. Among the white pines are the oldest-living trees, the worldÕs largest pines, species dependent on birds for seed dispersal, species important for grizzly bear habitat and species of high commercial timber value. The principal threats to white pine populations are blister rust (Cronartium ribicola, pathogen), fire suppression, succession, mountain pine beetle and climate change. Severe population declines in several white pine species are attributed to losses caused by these factors acting either alone or together, and sometimes in concert with logging and other land-use changes. The importance and particular interactions of these threats vary by region and species. For example, many northern and western populations of whitebark pine are seriously declining from a combination of mountain pine beetle outbreaks and severe blister rust infestations. As whitebark pines provide many keystone services on high-elevation sites, their loss would impact forest composition and structure, succession, biodiversity, and ecosystem services. Although there are serious challenges to science-based management and conservation (especially in remote American wilderness areas), prompt and effective intervention promoting regeneration of blister rust-resistant white pines could mitigate these severe impacts.

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