DOI: 10.5061/dryad.fxpnvx0p1
title: Data from: Influence of paleolithic range contraction, admixture and long-distance dispersal on genetic gradients of modern humans in Asia

description: Cavalli-Sforza and coauthors originally explored the genetic variation of
 modern humans throughout the world and observed an overall east-west
 genetic gradient in Asia. However, the specific environmental and
 population genetics processes causing this gradient were not formally
 investigated and promoted discussion in recent studies. Here we studied
 the influence of diverse environmental and population genetics processes
 on Asian genetic gradients and identified which could have produced the
 observed gradient. To do so, we performed extensive spatially-explicit
 computer simulations of genetic data under the following scenarios: (i)
 variable levels of admixture between Paleolithic and Neolithic
 populations, (ii) migration through long-distance dispersal (LDD), (iii)
 Paleolithic range contraction induced by the last glacial maximum (LGM)
 and, (iv) Neolithic range expansions from one or two geographic origins
 (the Fertile Crescent and the Yangzi and Yellow River Basins). Next, we
 estimated genetic gradients from the simulated data and we found that they
 were sensible to the analyzed processes, especially to the range
 contraction induced by LGM and to the number of Neolithic expansions. Some
 scenarios were compatible with the observed east-west genetic gradient,
 such as the Paleolithic expansion with a range contraction induced by the
 LGM or two Neolithic range expansions from both the east and the west. In
 general, LDD increased the variance of genetic gradients among
 simulations. We interpreted the obtained gradients as a consequence of
 both allele surfing caused by range expansions and
 isolation by distance along the vast east-west geographic axis of this
 continent.
description: ******* Simulated genetic data ******* Each
 folder is identified according to the scenario, and contains another
 folder with the input files (files *.txt, *.par, *.sam, *.asc) to simulate
 it, the corresponding simulated genetic data (files *.arp) and the derived
 PC maps (files *.png). A file with the locations of the samples is also
 included (coord.txt). * Pure Paleolithic expansion
 * <br> The folder “Paleo” contains the input files (INFILES), the
 genetic data and the corresponding PC maps simulated under the scenario of
 a pure Paleolithic expansion, ignoring the range contraction induced by
 the LGM and LDD events. * Pure Paleolithic expansion
 considering the range contraction induced by the LGM * <br> The
 folder “Paleo_REC” contains the input files (INFILES), the genetic data
 and the corresponding PC maps simulated under the scenario of a pure
 Paleolithic expansion suffering the range contraction induced by the
 LGM.  * Pure Paleolithic expansion considering
 long-distance dispersal (LDD) events * <br> The folder “Paleo_LDD”
 contains the input files (INFILES), the genetic data  and the
 corresponding PC maps simulated under the scenario of a pure Paleolithic
 expansion considering LDD events.  * Paleolithic
 expansion followed by two Neolithic expansions (IR=0) from Middle East and
 East Asia considering the range contraction induced by the LGM
 * <br> The folder “Paleo2NeoIR0_REC” contains the input files
 (INFILES), the genetic data and the corresponding PC maps simulated under
 the scenario of a Paleolithic expansion followed by two Neolithic
 expansions (IR=0) from Middle East and later from East Asia suffering the
 range contraction induced by the LGM.  * Paleolithic
 expansion followed by two Neolithic expansions (IR=0) from Middle East and
 East Asia considering LDD events * <br> The folder
 “Paleo2NeoIR0_LDD” contains the input files (INFILES), the genetic data
 and the corresponding PC maps simulated under the scenario of a
 Paleolithic expansion followed by two Neolithic expansions from Middle
 East and later from East Asia considering LDD events. 
 * Paleolithic expansion followed by a single Neolithic expansion
 (IR=0) from Middle East considering the range contraction induced by the
 LGM * <br> The folder “Paleo_MiddleEastNeoIR0_REC” contains the
 input files (INFILES), the genetic data and the corresponding PC maps
 simulated under the scenario of a Paleolithic expansion followed by a
 single Neolithic expansions (IR=0) from Middle East suffering the range
 contraction induced by the LGM.  * Paleolithic
 expansion followed by a single Neolithic expansion (IR=0) from East Asia
 considering the range contraction induced by the LGM * <br> The
 folder “Paleo_EastAsiaNeoIR0_REC” contains the input files (INFILES) and
 the corresponding PC maps simulated under the scenario of a Paleolithic
 expansion followed by a single Neolithic expansion (IR=0) from East Asia
 suffering the range contraction induced by the LGM.  *
 Paleolithic expansion followed by a single Neolithic expansion (IR=0) from
 Middle East considering LDD events * <br> The folder
 “Paleo_MiddleEastNeoIR0_REC” contains the input files  (INFILES), the
 genetic data and the corresponding PC maps simulated under the scenario of
 a Paleolithic expansion followed by a single Neolithic expansions (IR=0)
 from Middle East considering LDD events.  * Paleolithic
 expansion followed by a single Neolithic expansion (IR=0) from East Asia
 considering LDD events * <br> The folder “Paleo_EastAsiaNeoIR0_REC”
 contains the input files (INFILES) the genetic data and the corresponding
 PC maps simulated under the scenario of a Paleolithic expansion followed
 by a single Neolithic expansion (IR=0) from East Asia considering LDD
 events.  * Paleolithic expansion followed by a single
 Neolithic expansion (IR=0.04) from Middle East considering the range
 contraction induced by the LGM * <br> The folder
 “Paleo_MiddleEastNeoIR004_REC” contains the input files (INFILES), the
 genetic data and the corresponding PC maps simulated under the scenario of
 a Paleolithic expansion followed by a single Neolithic expansion (IR=0.04)
 from East Asia suffering the range contraction induced by the
 LGM.  * Paleolithic expansion followed by a single
 Neolithic expansion (IR=0.04) from East Asia considering the range
 contraction induced by the LGM * <br> The folder
 “Paleo_EastAsiaNeoIR0_REC” contains the input files (INFILES), the genetic
 data  and the corresponding PC maps simulated under the scenario of a
 Paleolithic expansion followed by a single Neolithic expansions (IR=0.04)
 from East Asia suffering the range contraction induced by the
 LGM.  * Paleolithic expansion followed by a single
 Neolithic expansion (IR=0.04) from Middle East considering LDD events
 * <br> The folder “Paleo_MiddleEastNeoIR004_REC” contains the input
 files (INFILES), the genetic data and the corresponding PC maps simulated
 under the scenario of a Paleolithic expansion followed by a single
 Neolithic expansion (IR=0.04) from East Asia considering LDD
 events.  * Paleolithic expansion followed by a single
 Neolithic expansion (IR=0.04) from East Asia considering LDD events
 * <br> The folder “Paleo_EastAsiaNeoIR0_REC” contains the input
 files  (INFILES), the genetic data and the corresponding PC maps simulated
 under the scenario of a Paleolithic expansion followed by a single
 Neolithic expansions (IR=0.04) from East Asia considering LDD
 events.