Data from: Genetic consequences of population expansions and contractions in the common hippopotamus (Hippopotamus amphibius) since the Late Pleistocene

Stoffel C, Dufresnes C, Okello JBA, Noirard C, Joly P, Nyakaana S, Muwanika VB, Alcala N, Vuilleumier S, Siegismund HR, Fumagalli L

Date Published: March 31, 2015

DOI: http://dx.doi.org/10.5061/dryad.4cv02

 

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Title XML file for molecular calibration analysis
Downloaded 3 times
Description XML file used in BEAST for the molecular calibration analysis of CR H. amphibius sequences, using the split with H. liberiensis (sequence OGR) as a reference.
Download MolecularCalibration.xml (114.6 Kb)
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Title XML for EBSP analysis
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Description XML file used in BEAST for the Extended Bayesian Skyline Plot (EBSP) analysis of H. amphibius, based on control region, cytochrome-b and nuclear HMG-2 sequences
Download EBSP.xml (349.4 Kb)
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Title Codes used for EBSP simulation analyses
Downloaded 11 times
Description Set of codes used for generating simulated datasets and performing EBSP analyses. File "ms_beast.R" runs the coalescent simulator MS (via package "phyclust" providing a R version of MS) to generate sequences from the template file "testalt_template" and create XML input files for use in BEAST. File "run.sh" runs these XML inputs in BEAST. File "plots.R" is used to visualize generated skyline plots.
Download EBSP_simulations.zip (15.62 Kb)
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Title Sequence alignments
Downloaded 2 times
Description FASTA alignments of all H. amphibius' sequences included in this study: mitochondrial control region ("Hippo_CR_all.fas"), cytochome-B ("Hippo_cytB_all.fas") and nuclear HMG-2 (Hippo_Nucl_all.fas"). Taxon ID are listed in Supplementary Table S1.
Download SequenceAlignments.zip (7.211 Kb)
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When using this data, please cite the original publication:

Stoffel C, Dufresnes C, Okello JBA, Noirard C, Joly P, Nyakaana S, Muwanika VB, Alcala N, Vuilleumier S, Siegismund HR, Fumagalli L (2015) Genetic consequences of population expansions and contractions in the common hippopotamus (Hippopotamus amphibius) since the Late Pleistocene. Molecular Ecology 24(10): 2507-2520. http://dx.doi.org/10.1111/mec.13179

Additionally, please cite the Dryad data package:

Stoffel C, Dufresnes C, Okello JBA, Noirard C, Joly P, Nyakaana S, Muwanika VB, Alcala N, Vuilleumier S, Siegismund HR, Fumagalli L (2015) Data from: Genetic consequences of population expansions and contractions in the common hippopotamus (Hippopotamus amphibius) since the Late Pleistocene. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.4cv02
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