A small strip of land between the Atlantic and Pacific ocean might seem like an odd place to look for answers about evolution. But, the Isthmus of Panama is considered to be one of the most important pieces of evidence in questions that involve the triggering of the last Ice Age, the separation of marine species, global ocean current circulation, and even the land connection between North and South America (O’Dea et al. 2016). Unfortunately, there is one problem. Scientists can’t necessarily agree on when the isthmus formed.
The isthmus was thought to have closed relatively rapidly around three million years ago (Ma), based on converging biological and geological evidence. Subduction of the Pacific Plate under the Caribbean Plate caused an underwater volcanic chain known as the Panama arc, which ended up moving westward with the movement of the South American Plate. This eventually closed the Central American Seaway and enabled the Great American Biotic Interchange, a massive land mammal migration (Stehli and Webb 1985, chaps. 2, 4, 5, 12). Additionally, seafloor cores showed that marine fossils (foraminifera) on either side of Panama began speciating 3.5 Ma (Keigwin 1978).
By the 1990s though, advances in molecular techniques allowed scientists to investigate whether the isthmus had formed gradually rather than all at once. One approach was to study marine species on opposite sides of the isthmus. The new land bridge that formed separated populations that had shared the same seaway, an example of allopatric speciation (Scott, 1916). As the newly isolated population accumulated genetic differences through mutation, natural selection, genetic drift, and gene flow, scientists could work backwards to estimate when they diverged. In 1993, a study comparing genetic differences in pairs of closely related snapping shrimp (Alpheus) on either side of the isthmus helped scientists estimate how long they had been evolving separately (Table 1). The findings were that some of the populations had diverged millions of years before the traditional 3 Ma timeline (Knowlton et al. 1993, 1629-32).
Table 1. Genetic divergence between seven pairs of snapping shrimp (Alpheus) from opposite sides of the Isthmus of Panama, measured using allozyme and mitochondrial DNA comparisons (Knowlton et al. 1993, 1630).

This evidence was one of several findings that challenged the original theory that the Isthmus of Panama closed relatively suddenly around 3 Ma (Bacon et al. 2015; Coates et al. 2013). Another clue came from uranium-lead dating technology which was not available previously. Researchers found minerals called zircons originating from Panama in sedimentary rocks dating back 13 to 15 Ma. Since these minerals could have been transported there by rivers flowing from the Panama arc, this means that parts of the isthmus had already emerged above sea level and had become connected to South America much earlier than previously thought (Montes et al., 2015).

Figure 1. Reconstruction of the Panama arc and northwestern South America during the middle Miocene (13 to 15 Ma), which shows the region’s geography and zircon deposits during an earlier stage of the formation. At least a segment of the Panama arc had emerged meaning the isthmus did not quickly solidify or close 3 Ma (Montes et al., 2015).
So, are Panama’s shrimp telling time right? They’re not necessarily wrong, but each piece of evidence is telling a different part of the story. The shrimps’ genetic differences were recorded when populations had begun evolving separately (3 Ma), but zircon deposits revealed how early parts of Panama had emerged and connected with South America (13-15 Ma). Neither provides a single date for the formation of the entire isthmus. Instead the evidence points to a staggered development of the land bridge, with the scientists having to work out when the process started, when the marine populations separated, and finally, when and how the isthmus actually got to its present form.
References
Bacon, Christine D., Daniele Silvestro, Carlos Jaramillo, Brian Tilston Smith, Prosanta Chakrabarty, and Alexandre Antonelli. “Biological Evidence Supports an Early and Complex Emergence of the Isthmus of Panama.” Proceedings of the National Academy of Sciences 112, no. 19 (2015): 6110–15. https://doi.org/10.1073/pnas.1423853112.
Coates, Anthony G., and Robert F. Stallard. “How Old Is the Isthmus of Panama?” Bulletin of Marine Science 89, no. 4 (2013): 801–13. https://doi.org/https://doi.org/10.5343/bms.2012.1076.
Knowlton, Nancy, Lee A. Weight, Luis Aníbal Solórzano, DeEtta K. Mills, and Eldredge Bermingham. “Divergence in Proteins, Mitochondrial DNA, and Reproductive Compatibility Across the Isthmus of Panama.” Science 260, no. 5114 (1993): 1629–32. http://www.jstor.org/stable/2881712.
Keigwin, Lloyd D. “Pliocene Closing of the Isthmus of Panama, Based on Biostratigraphic Evidence from Nearby Pacific Ocean and Caribbean Sea Cores.” Geology 6, no. 10 (1978): 630. https://doi.org/10.1130/0091-7613(1978)6%3C630:PCOTIO%3E2.0.CO;2.
Montes, C., A. Cardona, C. Jaramillo, et al. “Middle Miocene Closure of the Central American Seaway.” Science 348, no. 6231 (2015): 226–29. https://doi.org/10.1126/science.aaa2815.
O’Dea, Aaron, Harilaos A. Lessios, Anthony G. Coates, et al. “Formation of the Isthmus of Panama.” Science Advances 2, no. 8 (2016): e1600883. https://doi.org/10.1126/sciadv.1600883.
Scott, W. B. “The Isthmus of Panama in Its Relation to the Animal Life of North and South America.” Science 43, no. 1100 (1916): 113–24. http://www.jstor.org/stable/1640614.
Stehli, Francis G., and S. David Webb. 1985. The Great American Biotic Interchange. Plenum Press.
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