Genetic diversity is necessary for evolutionary response to changing environmental conditions such as those facing many threatened and endangered species. To investigate the relationship between genetic diversity and conservation status, we conducted a systematic, quantitative review of vertebrate microsatellite data published since 1990: we screened 5165 previously published articles and identified 1941 microsatellite datasets spanning 17,988 loci that characterized wild populations distributed among five vertebrate classes. We analyzed these data in the context of conservation by comparing empirical estimates of heterozygosity and allelic richness between threatened and non-threatened species. We found that both heterozygosity and allelic richness are reduced in threatened species, suggesting that inbreeding and drift are both effective at removing genetic diversity in endangered populations. We then considered the criteria typically used to rank species of conservation concern (including declining population size, species range extent, and the number of mature individuals) to determine which of these criteria are most effective at identifying genetically depauperate species. However, we found that the existing criteria failed to systematically identify populations with low genetic diversity. To rectify this, we suggest a novel approach for identifying species of conservation need by estimating the expected loss of genetic diversity. We then evaluated the efficacy of our new approach and found that it performs significantly better than the existing methods for identifying species that merit conservation concern in part because of reduced genetic diversity.

Biologists routinely use molecular markers to identify conservation units, to quantify genetic connectivity, to estimate population sizes, and to identify targets of selection. Many imperiled eagle populations require such efforts and would benefit from enhanced genomic resources. We sequenced, assembled, and annotated the first eagle genome using DNA from a male golden eagle (Aquila chrysaetos) captured in western North America. We constructed genomic libraries that were sequenced using Illumina technology and assembled the high-quality data to a depth of ∼40x coverage. The genome assembly includes 2,552 scaffolds >10 Kb and 415 scaffolds >1.2 Mb. We annotated 16,571 genes that are involved in myriad biological processes, including such disparate traits as beak formation and color vision. We also identified repetitive regions spanning 92 Mb (∼6% of the assembly), including LINES, SINES, LTR-RTs and DNA transposons. The mitochondrial genome encompasses 17,332 bp and is ∼91% identical to the Mountain Hawk-Eagle (Nisaetus nipalensis). Finally, the data reveal that several anonymous microsatellites commonly used for population studies are embedded within protein-coding genes and thus may not have evolved in a neutral fashion. Because the genome sequence includes ∼800,000 novel polymorphisms, markers can now be chosen based on their proximity to functional genes involved in migration, carnivory, and other biological processes.

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