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Abstract

Despite decades of research, the roles of climate and humans in driving the dramatic extinctions of large-bodied mammals during the Late Quaternary period remain contentious. Here we use ancient DNA, species distribution models and the human fossil record to elucidate how climate and humans shaped the demographic history of woolly rhinoceros, woolly mammoth, wild horse, reindeer, bison and musk ox. We show that climate has been a major driver of population change over the past 50,000 years. However, each species responds differently to the effects of climatic shifts, habitat redistribution and human encroachment. Although climate change alone can explain the extinction of some species, such as Eurasian musk ox and woolly rhinoceros, a combination of climatic and anthropogenic effects appears to be responsible for the extinction of others, including Eurasian steppe bison and wild horse. We find no genetic signature or any distinctive range dynamics distinguishing extinct from surviving species, emphasizing the challenges associated with predicting future responses of extant mammals to climate and human-mediated habitat change. © 2011 Macmillan Publishers Limited. All rights reserved

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IntCal09 and Marine09 Radiocarbon Age Calibration Curves, 0–50,000 Years cal BP

P J Reimer, M. G. L. Baillie, E Bard … (2009)

The IntCal04 and Marine04 radiocarbon calibration curves have been updated from 12 cal kBP (cal kBP is here defined as thousands of calibrated years before AD 1950), and extended to 50 cal kBP, utilizing newly available data sets that meet the IntCal Working Group criteria for pristine corals and other carbonates and for quantification of uncertainty in both the14C and calendar timescales as established in 2002. No change was made to the curves from 0–12 cal kBP. The curves were constructed using a Markov chain Monte Carlo (MCMC) implementation of the random walk model used for IntCal04 and Marine04. The new curves were ratified at the 20th International Radiocarbon Conference in June 2009 and are available in the Supplemental Material atwww.radiocarbon.org.

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Smooth skyride through a rough skyline: Bayesian coalescent-based inference of population dynamics.

Vladimir N. Minin, Erik W Bloomquist, Marc Suchard (2008)

Kingman's coalescent process opens the door for estimation of population genetics model parameters from molecular sequences. One paramount parameter of interest is the effective population size. Temporal variation of this quantity characterizes the demographic history of a population. Because researchers are rarely able to choose a priori a deterministic model describing effective population size dynamics for data at hand, nonparametric curve-fitting methods based on multiple change-point (MCP) models have been developed. We propose an alternative to change-point modeling that exploits Gaussian Markov random fields to achieve temporal smoothing of the effective population size in a Bayesian framework. The main advantage of our approach is that, in contrast to MCP models, the explicit temporal smoothing does not require strong prior decisions. To approximate the posterior distribution of the population dynamics, we use efficient, fast mixing Markov chain Monte Carlo algorithms designed for highly structured Gaussian models. In a simulation study, we demonstrate that the proposed temporal smoothing method, named Bayesian skyride, successfully recovers "true" population size trajectories in all simulation scenarios and competes well with the MCP approaches without evoking strong prior assumptions. We apply our Bayesian skyride method to 2 real data sets. We analyze sequences of hepatitis C virus contemporaneously sampled in Egypt, reproducing all key known aspects of the viral population dynamics. Next, we estimate the demographic histories of human influenza A hemagglutinin sequences, serially sampled throughout 3 flu seasons.

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The late Pleistocene dispersal of modern humans in the Americas.

Ted Goebel, Michael R Waters, Dennis H O'Rourke (2008)

When did humans colonize the Americas? From where did they come and what routes did they take? These questions have gripped scientists for decades, but until recently answers have proven difficult to find. Current genetic evidence implies dispersal from a single Siberian population toward the Bering Land Bridge no earlier than about 30,000 years ago (and possibly after 22,000 years ago), then migration from Beringia to the Americas sometime after 16,500 years ago. The archaeological records of Siberia and Beringia generally support these findings, as do archaeological sites in North and South America dating to as early as 15,000 years ago. If this is the time of colonization, geological data from western Canada suggest that humans dispersed along the recently deglaciated Pacific coastline.