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Mitochondrial DNA is commonly used in population genetic studies to investigate spatial structure, intraspecific variation, and phylogenetic relationships. The control region is the most rapidly evolving and largest non-coding region, but its analysis can be complicated by heteroplasmic signals of genome duplication in many mammals, including felids. Here, we describe the presence of heteroplasmy in the control region of Canada lynx (Lynx canadensis) through intra-individual sequence variation. Our results demonstrate multiple haplotypes of varying length in each lynx, resulting from different copy numbers of the repetitive sequence RS-2 and suggest possible heteroplasmic single nucleotide polymorphisms in both repetitive sequences RS-2 and RS-3. Intra-individual variation was only observed in the repetitive sequences while inter-individual variation was detected in the flanking regions outside of the repetitive sequences, indicating that heteroplasmic mutations are restricted to these repeat regions. Although each lynx displayed multiple haplotypes of varying length, we found the most common variant contained three complete copies of the RS-2 repeat unit, suggesting copy number is regulated by stabilizing selection. While genome duplication offers potential for increased diversity, heteroplasmy may lead to a selective advantage or detriment in the face of mitochondrial function and disease, which could have significant implications for wildlife populations experiencing decline (e.g., bottlenecks) as a result of habitat modification or climate change. [ABSTRACT FROM AUTHOR]

Abstract: Restoration of degraded landscapes has become necessary to reverse the pervasive threats from human exploitation. Restoration requires first the monitoring of progress toward any chosen goals to determine their resilience and persistence, and second to conduct in a comparable adjacent area but with less human impact the restoration of trophic structures and ecosystem processes to act as reference systems (controls) with which we compare the viability of the chosen goal. We present here the rationale and a method for predicting the trajectory of restoration and assessing its progress toward a predetermined state, the endpoint, using a restoration index. This assessment of restoration requires that we know when a predetermined endpoint has been achieved and whether the envisioned community of species and their interactions can be restored. The restoration index can use species’ presence or density, and the rate of change of ecosystem processes. The index applies to trophic levels, functional groups, successional stages, alternative states, and novel ecosystems. Also, our method allows measurement of the resilience of ecosystems to disturbance, a desired property for conservation and management. We provide global examples to illustrate these points. [ABSTRACT FROM AUTHOR]