Problems with interspecific methods at   the intraspecific level Evolutionary relationships above and below the   species level are different in nature. Relationships between genes sampled   from individuals belonging to different species (phylogeny sensu stricto) are   hierarchical. This is because they are the product of reproductive isolation and   population fission over longer timescales, during which mutation combined   with population divergence led to the fixation of different alleles and,   ultimately, to nonoverlapping gene pools. By contrast, relationships between   genes sampled from individuals within a species (sometimes called TOKOGENY²)   are not hierarchical, because they are the result of sexual reproduction, of   smaller numbers of relatively recent mutations and, frequently, of recombination   (Fig. 1). More traditional methods developed to estimate interspecific   relationships, such as maximum likelihood, maximum parsimony and minimum   evolution, cannot properly take account of the fact that, at the population   level, several phenomena violate some of their assumptions. This leads to   poor resolution or inadequately portrays genealogical relationships

种间研究方法去研究种上和种下的进化关系所存在的问题在本质上是不同的。从属于不同物种个体中提取的基因之间的关系是级联式的，这是狭义的系统发育。它们是在较长时间内生殖隔离和种群分裂的产物，在此过程中，突变和种群分化导致不同等位基因的固定，最终导致互不重叠的基因库。相比之下，从一个物种内的不同个体中提取的基因之间的关系（有时称为TOKOGENY）不是级联关系，因为它们是有性生殖的结果，相对较新的突变数量较少，而且经常是重组的结果（图1）。为了估计种间关系而开发的传统方法，如最大似然法、最大简约法和最小进化法，不能适当地考虑到在种群水平上，一些现象违反了它们的一些假设。这会导致解决方案不好或无法充分描述谱系关系。