The prior definition of populations,   usually defined geographically, is a critical step in all of these methods,   although the focus on individual organisms rather than a preconceived   interbreeding “group” would be more objective for species delimitation (Vrana   and Wheeler, 1992). Current methods for estimating population coherence from   the sequences themselves rely on evidence for recombination to determine   species limits (Doyle,   1995) but are impractical for large-scale analysis at present. An   alternative possibility to detect species separation is to search for   discontinuities in sequence variation associated with the species boundaries.   For example, statistical parsimony analysis (Templeton et al., 1992)   separates groups of sequences into different sequence networks if genotypes   are connected by comparatively long branches that are affected by homoplasy.   Although homoplasious connections do not necessarily correspond to species   boundaries, in practice this algorithm often does separate groups that are   roughly coincident with named species or species groups (e.g., Cardoso and   Vogler, 2005; Templeton, 2001; Wilder and Hollocher, 2003; Templeton et al.,   1995), and the WP method for species delimitation is now recommended to be   applied only in conjunction with statistical parsimony analysis in order to   reduce the complexity of large data sets (Sites and Marshall, 2003).

之前从地理学角度对种群进行定义，通常是所有这些方法中的一个关键步骤，尽管将重点放在有机个体上，而不是预先确定的杂交“群体”，对于物种定界更为客观（Vrana and Wheeler, 1992）。目前从序列本身估计种群一致性的方法依赖于重组的证据来确定物种的限制（Doyle, 1995），但对于目前的大规模分析来说是不切实际的。检测物种分隔的另一种可能性是寻找与物种边界相关的序列变异的不连续性。例如，统计简约分析（Templeton et al., 1992）将较长分支连接的序列分组为不同的序列网络，该分支通常主要是由非同源相似基因型导致。尽管非同源相似性联结并不一定对应于物种边界，但在实践中，该算法得到的分群通常已命名物种或种组大致一致（例如，Cardoso and Vogler, 2005; Templeton, 2001; Wilder and Hollocher,   2003; Templeton et al., 1995）。物种定界的WP方法现在建议仅与统计简约分析结合使用，以减少大型数据集的复杂性（Sites and Marshall, 2003）。