Here is a series of articles that, in my opinion, are required reading in evolutionary biology and others that I have found interesting to read. This does not represent an exhaustive list, over time I will expand it

"Homology" in proteins and nucleic acids: A terminology muddle and way out of it

Gerald R.Reeck, Christophde Haën, David C. Teller, Russell F.Doolittle, Walter M.Fitch, Richard E. Dickerson, Pierre Chambon, Andrew D.McLachlan, Emanuel Margoliash, Thomas H. Jukes, Emile Zuckerkandl. Cell 1987, 50: 667. Link

This comment clarifies the difference between homology and similarity in DNA or protein sequences. Additionally, it describes three situations in which hazards arise by using homology to mean similarity.

Distinguishing homologous from analogous proteins

Walter M. Fitch. Systematic Biology 1970, 19: 99. Link

This work provides a means by which it is possible to determine whether two groups of related proteins have a common ancestor or are of independent origin, including the definition of orthology and paralogy.

Fitting the gene lineage into its species lineage, a parsimony strategy Illustrated by cladograms constructed from globin sequences

Morris Goodman, John Czelusniak, G. William Moore, A. E. Romero-Herrera & Genji Matsuda. Systematic Zoology 1979, 28: 132. Link

In this work, Morris Goodman et al. show how the duplicative history of genes can be inferred by comparing gene trees with species trees.

New perspectives in the molecular biological analysis of mammalian phylogeny

Morris Goodman, C.B. Olson, J.E. Beeber & John Czelusniak. Acta Zoologica Fennica 1982, 169: 19. Link

This work represents the seminal paper in which the famous Goodman-Bremer support methodology is described.

Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints

Danilo A. Tagle, Benn F. Koop, Morris Goodman, Jerry L. Slightom, David L. Hess, Richard T. Jones. Journal of Molecular Biology 1988, 203: 439. Link

In this work, Tagle et al. introduce the term “phylogenetic footprinting” to describe the phylogenetic comparisons that reveal conserved cis- elements in the non-coding regions of homologous genes.

Possible Relation between Deoxyribonucleic Acid and Protein Structures

George Gamow. Nature 1954, 173: 318. Link

Positive selection causes purifying selection

Morris Goodman. Nature 1982, 295: 630. Link

Natural selection and elimination

C. Lloyd Morgan. Nature 1888, 38: 370. Link

Evolution at two levels in humans and chimpanzees

Mary-Claire King & Allan C. Wilson. Science 1975, 188: 107. Link

Enzyme polymorphisms in man

Harry Harries. Proceedings of the Royal Society of London. Series B, Biological sciences 1966, 164: 298. Link

A molecular approach to the study of genic heterozygosity in natural populations. II. Amount of variation and degree of heterozygosity in natural populations of Drosophila pseudoobscura

Richard C. Lewontin & John L. Hubby. Genetics 1966, 54: 595. Link

Primary structure and evolution of cytochrome c

Emanuel Margoliash. Proceedings of the National Academy of Sciences of the United States of America. 1963, 50: 672. Link

Amino-acid sequence investigations of fibrinopeptides from various mammals: evolutionary implications

Russell F. Doolittle & Birger Blombäck . Nature. 1964, 202: 147. Link

Evolutionary divergence and convergence in proteins

Emile Zuckerkandl & Linus Pauling . Evolving Genes and Proteins. 1965, 97 Link

Evolutionary rate at the molecular level

Motoo Kimura . Nature. 1968, 217: 624. Link

Non-Darwinian evolution

Jack L. King & Thomas H. Jukes . Science. 1969, 164: 788. Link