Why can’t the evolutionary relationships between certain species be explained thoroughly?

Phylogeny: It is related to evolution dealings in the evolutionary development of a species. It is represented by different ways vertical or slanted.  

Phylogenesis: It refers to the evolutionary relationships among species.  

Phylogenetics: It is determination or estimation of evolutionary relationships among groups of species, organisms and genes.  

Phylogenetics is a field of biology which is used to find relationships among different organisms. This relationship is showing through a tree (used to model actual evolutionary relationship of organisms). Ancestral divided into two descendant species because closely related organisms are shown in near branches. If there is too much divergence between two species its mean they are not closely related.  

The history of speciation (one species becomes divided into more than one new species) tells us how these species are related to each other. If they evolve to be separate species relatively recently then they are "closely relative" similarly if they evolve to be separate specie long above then they are "distant relatives". For example orthologs are genes in different species that evolved from common ancestor gene by speciation; they retain same function in the course of evolution.

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