Reevaluating human colonization of the Caribbean using chronometric hygiene and Bayesian modeling

Human settlement of the Caribbean represents the only example in the Americas of peoples colonizing islands that were not visible from surrounding mainland areas or other islands. Unfortunately, many interpretive models have relied on radiocarbon determinations that do not meet standard criteria for reporting because they lack critical information or sufficient provenience, often leading to specious interpretations. We have collated 2484 radiocarbon determinations, assigned them to classes based on chronometric hygiene criteria, and constructed Bayesian colonization models of the acceptable determinations to examine patterns of initial settlement. Colonization estimates for 26 islands indicate that (i) the region was settled in two major population dispersals that likely originated from South America; (ii) colonists reached islands in the northern Antilles before the southern islands; and (iii) the results support the southward route hypothesis and refute the “stepping-stone model.”

Tom70 enhances mitochondrial preprotein import efficiency by binding to internal targeting sequences

The biogenesis of mitochondria depends on the import of hundreds of preproteins. N-terminal matrix-targeting signals (MTSs) direct preproteins to the surface receptors Tom20, Tom22, and Tom70. In this study, we show that many preproteins contain additional internal MTS-like signals (iMTS-Ls) in their mature region that share the characteristic properties of presequences. These features allow the in silico prediction of iMTS-Ls. Using Atp1 as model substrate, we show that iMTS-Ls mediate the binding to Tom70 and have the potential to target the protein to mitochondria if they are presented at its N terminus. The import of preproteins with high iMTS-L content is significantly impaired in the absence of Tom70, whereas preproteins with low iMTS-L scores are less dependent on Tom70. We propose a stepping stone model according to which the Tom70-mediated interaction with internal binding sites improves the import competence of preproteins and increases the efficiency of their translocation into the mitochondrial matrix.

Isolation-By-Distance-and-Time in a stepping-stone model

With the great advances in ancient DNA extraction, population genetics data are now made of geographically separated individuals from both present and ancient times. However, population genetics theory about the joint effect of space and time has not been thoroughly studied. Based on the classical stepping--stone model, we develop the theory of Isolation by Distance and Time. We derive the correlation of allele frequencies between demes in the case where ancient samples are present in the data, and investigate the impact of edge effects with forward-in-time simulations. We also derive results about coalescent times in circular/toroidal models. As one of the most common way to investigate population structure is to apply principal component analysis, we evaluate the impact of this theory on plots of principal components. Our results demonstrate that time between samples is a non-negligible factor that requires new attention in population genetics.

Stepping-Stone Model with Circular Brownian Migration

In this paper we consider the stepping-stone model on a circle with circular Brownian migration. We first point out a connection between Arratia flow on the circle and the marginal distribution of this model. We then give a new representation for the stepping-stone model using Arratia flow and circular coalescing Brownian motion. Such a representation enables us to carry out some explicit computations. In particular, we find the distribution for the first time when there is only one type left across the circle.