Skip to main content
Dryad logo

Data from: Influence of paleolithic range contraction, admixture and long-distance dispersal on genetic gradients of modern humans in Asia

Citation

Branco, Catarina; Arenas, Miguel; Currat, Mathias; Ray, Nicolas (2020), Data from: Influence of paleolithic range contraction, admixture and long-distance dispersal on genetic gradients of modern humans in Asia, Dryad, Dataset, https://doi.org/10.5061/dryad.fxpnvx0p1

Abstract

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.

Usage Notes

******* 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 * 
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 * 
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 * 
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 * 
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 * 
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 * 
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 * 
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 * 
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 * 
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 * 
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 * 
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 * 
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 * 
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.

Funding

Fundação para a Ciência e a Tecnologia, Award: SFRH/BD/143607/2019

Swiss National Science Foundation, Award: 31003A_182577

Ministerio de Economía y Competitividad, Award: RYC-2015-18241

Swiss National Science Foundation, Award: 31003A_182577