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Species responses are influenced by processes operating at multiple scales, yet many conservation studies and management actions are focused on a single scale.
Many conservation studies over recent decades have empirically measured genetic parameters such as allelic diversity or heterozygosity over time (Nielsen et al. 1997; Spencer et al. 2000; Vilà et al. 2003; Zhu et al.
Building on the metapopulation theory, many conservation studies use patch area and structural connectivity measures as indicators of population size and isolation, respectively, two components with major demographic and genetic effects on the short- and long-term viability of species systems (e.g. [ 31- 33]).
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Despite the wide variety of topics, in many conservation genetic studies, neutral molecular markers, like amplified fragment length polymorphisms (AFLPs) and microsatellites, are applied.
However, because of the difficulty of isolating genetic markers and the considerable cost and time associated with extensive genotyping of individuals in populations, many conservation-genetic studies have employed relatively small numbers of genetic loci, such as RFLPs, AFLPs, and SSRs (simple sequence repeats, or microsatellites).
Many conservation approaches work by selecting species for conservation (see e.g. [ 41]).
In this paper, we demonstrate that readily attainable unfinished draft-quality genome sequences have high potential value and utility for many conservation, ecological, and evolutionary studies of nonmodel organisms.
It also implies that the current conservation studies may have missed many conserved regions by calculating conservation scores based on genome alignments.
It is thus evident that many conserved regions are neglected by the current conservation studies.
The cross species transferability provides a potential source of codominant markers for many related species and facilitates evolutionary, ecological, and conservation studies across the species.
First, many functional regions can be easily missed by the current conservation studies while they are identified by our method based on the new measurement.
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