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Measuring the correctness of a phylogenetic tree is one of the most fundamental tasks in phylogenetic study. A large number of methods have been proposed to measure the correctness of a tree. Such methods completely depend on the reference tree and they compute the distance between reference the tree and the target tree. But it is very difficult to obtain a precise and an accurate reference tree for a selected dataset. As a result, the existing methods for comparing the phylogenetic trees can behave unexpectedly in various scenarios. In this paper, we introduce a scoring function, called the Deformity Index, to measure the correctness of a tree based on the biological knowledge of the clades. The strength of our proposed method is that it does not consider any reference tree. We have also investigated the range and the distributions of the different modules of Deformity Index. Furthermore, we perform different goodness of fit tests to understand its cumulative distribution. We have also examined in detail the robustness as well as the scalability of our measure by different statistical tests under the Yule and the uniform models. Moreover, we show that our proposed scoring function can overcome the limitations of the conventional methods of tree comparing by experimenting on different biological datasets.

Measuring the correctness of a phylogenetic tree is one of the most fundamental tasks in phylogenetic study. A large number of methods have been proposed to measure the correctness of a tree. Such methods completely depend on the reference tree and they compute the distance between reference the tree and the target tree. But it is very difficult to obtain a precise and an accurate reference tree for a selected dataset. As a result, the existing methods for comparing the phylogenetic trees can behave unexpectedly in various scenarios. In this paper, we introduce a scoring function, called the Deformity Index, to measure the correctness of a tree based on the biological knowledge of the clades. The strength of our proposed method is that it does not consider any reference tree. We have also investigated the range and the distributions of the different modules of Deformity Index. Furthermore, we perform different goodness of fit tests to understand its cumulative distribution. We have also examined in detail the robustness as well as the scalability of our measure by different statistical tests under the Yule and the uniform models. Moreover, we show that our proposed scoring function can overcome the limitations of the conventional methods of tree comparing by experimenting on different biological datasets..

1The origin of modern human and their migration across the world is one of the most 2 debated topics for the decades. There exist two different hypotheses, recent African 3 origin and multi-regional evolution, based on the genomic studies, haplogroups, ar-4 chaeological records, cultural behaviors, palaeontology studies, etc. Various studies 5 placed the modern humans in a phylogenetic tree to depict the relationships among 6 them. However, the conflicts between the results obtained from the molecular data and 7 the archaeological and palaeontological reports still exist. We adopt a novel genomic 8 features derived from the whole mitochondrial sequence, and using them phylogenetic 9 trees are constructed providing a new insight on human migration. The results we 10 derived from the genomic feature is more consistent with the archaeological findings 11 based on the time of origin of different communities. We find that some Asian com-12 munities are placed at the basal point with a very high bootstrap score. This study 13 roughly estimates the existence of the archaic human at 4-5 million years ago and 14 presence of human in Africa at 800 kilo years ago. The basal position of the Asian 15 communities show some close relationships between the modern Asians and the archaic 16 humans along with the Africans. 17 19studied extensively. The multiple genetic admixtures due to the migration, intermarriage, slavery, 20 human trafficking etc. played an important role to make the human history very complex [1, 2]. 21Apart from that, different assumptions such as gene flow [3], make the study of human evolution 22 and migration more complex [4]. 23Broadly, there exist two hypotheses of the human evolution and migration. The "recent African 24 origin" or "replacement" hypothesis [5][6][7] states that there exist the anatomically modern humans 25 which subsequently replace the ancient humans and spread all over the world [8][9][10]. There are var-26 ious methods incorporated to describe the history of the humans. Several genomic studies [11-13] 27 supported the "replacement" hypothesis. This hypothesis proposes that there is no or very less 28 admixture or genetic mixing between AMH and the archaic humans throughout the world. But 29 this hypothesis is disproved by some recent studies [14, 15]. Alternatively, the "multi-regional" hy-30 pothesis [16] states that the evolution of the archaic human occurred in different parts of the world. 31This evolution ended up with the AMH. Several linguistic analysis [17,18], cultural analysis [19,20] 32 support the "multi-regional" hypotheses. 33 1 Though various genomic studies were conducted for searching the origin of humans, most of 34 the studies focused on the phylogenetic tree derived from alignment based methods [11,[21][22][23], 35 SNP genotyping [24, 25], or supertree based approach [1]. Since then, the conflicts between the 36 genomic studies and the archaeological and palaeontological studies exist in the study of the origin 37 of humans [26]. Many archaeologis...