Studying human and nonhuman primate evolutionary biology with powerful in vitro and in vivo functional genomics tools

Abstract

In recent years, tools for functional genomic studies have become increasingly feasible for use by evolutionary anthropologists. In this review, we provide brief overviews of several exciting in vitro techniques that can be paired with "-omics" approaches (e.g., genomics, epigenomics, transcriptomics, proteomics, and metabolomics) for potentially powerful evolutionary insights. These in vitro techniques include ancestral protein resurrection, cell line experiments using primary, immortalized, and induced pluripotent stem cells, and CRISPR-Cas9 genetic manipulation. We also discuss how several of these methods can be used in vivo, for transgenic organism studies of human and nonhuman primate evolution. Throughout this review, we highlight example studies in which these approaches have already been used to inform our understanding of the evolutionary biology of modern and archaic humans and other primates while simultaneously identifying future opportunities for anthropologists to use this toolkit to help answer additional outstanding questions in evolutionary anthropology.

Keywords: CRISPR-Cas9; ancestral protein reconstruction; cell lines; evolutionary genomics; iPSCs; in vitro assays; transgenic organisms.

Figure 1.. The potential of functional genomics techniques for investigating questions in evolutionary anthropology.

Individual images: Shutterstock and Phylopic.

Figure 2.. The ‘-omics’.

A schematic representation of the ‘-omics’ fields of genomics, epigenomics, transcriptomics, proteomics, and metabolomics, including depictions of the origins of the biological molecules that are the focus of each field of study and some of the technologies through which these data are produced. Individual images: BioRender.

Figure 3.. Induced pluripotent stem cells (iPSCs).

By collecting differentiated cells such as fibroblasts or melanocytes from humans or non-human primates and exposing them to reprogramming factor proteins, scientists can now create iPSCs, which can then be subsequently differentiated into many types of cells in the body for tissue-specific experiments and functional genomic analyses. Individual images: Shutterstock and Phylopic.

Figure 4.. Protein Reconstruction and Resurrection.

A) On the left, if DNA can be extracted and sequenced from ancient hominin or extinct non-human primate samples, then the amino acid sequences of ancient proteins can be inferred relatively directly based on gene coding region DNA sequences. On the right, if ancient genomes are unavailable, ancestral protein sequences can be reconstructed through computational analysis of sequences from extant species. B) The ancestral DNA sequence can then be synthesized and either inserted into an organism’s genome directly by genome editing to observe phenotypic effects or inserted into bacterial or mammalian cells in culture for experimental assays and characterization, either after extraction and purification of the protein or in the in vitro cell culture environment. Individual images: Shutterstock and Phylopic.

Figure 5.. How CRISPR-Cas9 can be used to edit genomes.

Schematic representation of how CRISPR gene-editing technology operates. (A) The Cas9 enzyme is guided by a ‘guide RNA (gRNA)’ in pink, which is specific to the target DNA sequence of interest. The Cas9 enzyme then creates a double-stranded break (DSB) in the unedited DNA (in green) at the site specific to the gRNA, which is then repaired in one of two natural, DNA-repair mechanisms: non-homologous end joining (NHEJ) or homology-directed repair (HDR). In NHEJ, the ends of the DSB are joined back together without the need for a template, often resulting in the insertion or deletion of various numbers of nucleotides (in black and gray). Thus, NHEJ typically causes a frameshift mutation, knocking out the function of the gene. In contrast, HDR uses a template, or donor DNA provided by the scientist (in purple), as a guide to repairing the DSB. If the ends of the donor DNA match the sequence of DNA around the DSB, then HDR will use that donor DNA as a template, resulting in the desired insertion or edit (in purple). (B) CRISPR-Cas9 genome editing techniques can be used in cell culture or embryonic genomes. Individual images: Shutterstock.