Phylogenetic reconstruction is a fast-growing field that is enriched by different statistical approaches and by findings  and  applications  in  a  broad  range  of  biological  areas.  Fundamental  to  these  are  the  mathematical models used to describe the patterns of DNA base substitution and amino acid replacement. These may become some of the basic models for comparative genome research. We discuss these models, including the analysis of observed DNA base and amino acid mutation patterns, the concept of site heterogeneity, and the incorporation of structural biology data, all of which have become particularly important in recent years. We also describe the use  of  such  models  in  phylogenetic  reconstruction  and  statistical  methods  for  the  comparison  of  different models.

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Molecular evolution is the process of evolution at the scale of DNA, RNA, lect 2010 Evo gen develp and societyand proteins. Molecular evolution emerged as a scientific field in the 1960s as researchers from molecular biology, evolutionary biology and population genetics sought to understand recent discoveries on the structure and function of nucleic acids and protein. Some of the key topics that spurred development of the field have been the evolution of enzyme function, the use of nucleic acid divergence as a “molecular clock” to study species divergence, and the origin of non-functional or junk DNA. Recent advances in genomics, including whole-genome sequencing, high-throughput protein characterization, and bioinformatics have led to a dramatic increase in studies on the topic. In the 2000s, some of the active topics have been the role of gene duplication in the emergence of novel gene function, the extent of adaptive molecular evolution versus neutral drift, and the identification of molecular changes responsible for various human characteristics especially those pertaining to infection, disease, and cognition.Reference