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Message: <blockquote data-quote="l_raty" data-source="post: 3961969" data-attributes="member: 24811">Maybe this was simply not part of the authors' main preoccupations ?As I understand the paper, the primary objective here was to produce a reference (complete -- i.e., mostly nuclear) genome for a lark.They chose a bird from this particular spp mainly because it represents a small, highly isolated population, which they theorized had likely gone through a bottleneck when founded. When a population goes though a bottleneck, it loses genetic diversity, which increases the levels of homozygosity in the individuals that belong to it -- and high levels of homozygozity make the sequencing of nuclear DNA easier. (Because you have only one sequence to deal with, instead of two wherever the homologous chromosomes have different alleles.)I see no real suggestion that the prospect of clarifying the relationships of the spp weighted particularly heavily on this choice.</blockquote>