Monday, October 26, 2015

Academic Bun Fight: Panama Isthmus Closed Earlier Than Currently Thought (or did it)

Biological evidence supports an early and complex emergence of the Isthmus of Panama

Bacon et al


The linking of North and South America by the Isthmus of Panama had major impacts on global climate, oceanic and atmospheric currents, and biodiversity, yet the timing of this critical event remains contentious. The Isthmus is traditionally understood to have fully closed by ca. 3.5 million years ago (Ma), and this date has been used as a benchmark for oceanographic, climatic, and evolutionary research, but recent evidence suggests a more complex geological formation. Here, we analyze both molecular and fossil data to evaluate the tempo of biotic exchange across the Americas in light of geological evidence. We demonstrate significant waves of dispersal of terrestrial organisms at approximately ca. 20 and 6 Ma and corresponding events separating marine organisms in the Atlantic and Pacific oceans at ca. 23 and 7 Ma. The direction of dispersal and their rates were symmetrical until the last ca. 6 Ma, when northern migration of South American lineages increased significantly. Variability among taxa in their timing of dispersal or vicariance across the Isthmus is not explained by the ecological factors tested in these analyses, including biome type, dispersal ability, and elevation preference. Migration was therefore not generally regulated by intrinsic traits but more likely reflects the presence of emergent terrain several millions of years earlier than commonly assumed. These results indicate that the dramatic biotic turnover associated with the Great American Biotic Interchange was a long and complex process that began as early as the Oligocene–Miocene transition.
That was a bad analysis!!!

Appearance of an early closure of the Isthmus of Panama is the product of biased inclusion of data in the metaanalysis




In their PNAS article “Biological evidence supports an early and complex emergence of the Isthmus of Panama,” Bacon et al. (1) use data from molecular comparisons of terrestrial and marine organisms taken from the literature to estimate dates of rate shifts in migration. One of their conclusions is that “events separating marine organisms in the Atlantic and Pacific oceans [occurred] at ca. 23 and 7 Ma” (1). The authors base this conclusion on two kinds of molecular dating: (i) 31 dates from phylogenies with evolutionary rates calibrated from fossils at one or more nodes, and (ii) 52 dates from mitochondrial divergence between sister species on either side of the Isthmus taken from the review by Lessios (2) (note: complete data are available from the Dryad Digital Repository). For the latter, divergence was converted to time by assuming a mitochondrial DNA divergence rate of 2% per million years. Unfortunately, Bacon et al.’s (1) metaanalysis of separations of marine organisms contains unexplained omissions of data and mistakes. Nine of the fossil calibrated divergence values are wrong, and three are omitted (though present in publications used to derive other dates). Thirty-eight comparisons from Lessios (2) are excluded. Criteria for inclusion of data are not stated but, judging from the estimated dates, only data from Cytochrome c oxidase subunit 1 were taken into account, even though Lessios (2) presents data for multiple mitochondrial genes. This selectivity in the marine dataset of Bacon et al. (1) is hard to explain, because the terrestrial data come from various genes, and because eight comparisons of Cytochrome c oxidase subunit 1 of marine species are among those excluded.
no!  it wasn't, damnit!
Reply to Lessios and Marko et al.: Early and progressive migration across the Isthmus of Panama is robust to missing data and biases


Bacon et al


The emergence of the Isthmus of Panama left a major imprint on the biodiversity of the Americas. The connection between South and North America facilitated dispersal of terrestrial and freshwater organisms, while separating marine species between the eastern Pacific and Caribbean seas. Recent geological data have questioned the long-standing view of a Pliocene emergence of the Isthmus (1) and show that the Central American Seaway, defined as the deep oceanic seaway along the tectonic boundary of the South American plate and Panama arc, was already closed by 15–13 Ma (2). Caribbean–Pacific shallow water exchange probably continued, albeit intermittently, until a full closure at 3.5 Ma (1–3). Recently Bacon et al. (3) used molecular and fossil data to evaluate the timing, tempo, and directionality of biotic exchange and vicariance across the Isthmus, and tested whether biological data are congruent with recent geological evidence. Significant increases in terrestrial dispersals were found at ca. 20 and 6 Ma, and increases in marine vicariance at ca. 23 and 7 Ma. Similar patterns prevailed despite intrinsic differences among the taxonomic groups surveyed. This led Bacon et al. (3) to reject the assumption of a single closure of the Isthmus at ca. 3.5 Ma in favor of an older, more complex model of land emergence and biotic interchange.

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