Proboscidean Diversity Project

These data complement the publication: "A comprehensive genomic history of extinct and living elephants" (Palkopoulou et al, PNAS, 2018)

Update history:
Sat Jan 18 22:28:21 EST 2020: minor updates
Tue Aug 28 18:38:13 EDT 2018: add .bai pointers
Wed Jan 31 23:53:51 EST 2018: minor edits
Thu Aug 9 14:44:23 EDT 2018: update pointers
Wed Jan 31 23:53:20 EST 2018: minor edits
Wed Jan 24 14:58:02 EST 2018: minor mods
Wed Jan 24 14:56:02 EST 2018: initial page construction

Latest version:

Version 1: The dataset has been reprocessed as described in Palkopoulou et al (2018), (Supplementary Information Notes 4 and 5). Data are available in several forms:


(A) Raw sequence data

 (A1) Original sequence data (in bam format) for elephantid samples sequenced in Palkopoulou et al, 2018 are available through the European Nucleotide Archive under accession number PRJEB24361,
(A2) Raw sequence data for some of these samples are available through ENA projects PRJNA281811, PRJNA301482 (Lynch et al. 2015; and Reddy et al., J.Biosci. 2015, respectively),
(A3) Original sequence data (in bam format) for some of these samples are available through ENA projects PRJEB7929, PRJEB18563 (Palkopoulou et al., 2015; and Meyer et al., 2017, respectively).

(B) Reference genome

 The most recent update (that we currently know) of the savanna elephant reference genome (LoxAfr4) is availablel at: ftp://ftp.broadinstitute.org/pub/assemblies/mammals/elephant/loxAfr4/. However, it is worth checking the UCSC genome browser, in case there have been new releases.

(C) Alignments

 Alignments files are very large. Depending on your connection, it may take a very long time (i.e. hours/days) to download a single file.

Description Download pointer (bam) Download pointer (bai) Size (bam) Notes
E. maximus_L L-Pavarthy_loxAfr4com_v2_dedup.RG.bam/ L-Pavarthy_loxAfr4com_v2_dedup.RG.bam.bai/ 56 Gb Re-processed data from Lynch et al. (2015)
E. maximus_M M-Asha_loxAfr4com_v2_dedup.RG.bam/ M-Asha_loxAfr4com_v2_dedup.RG.bam.bai/ 63 Gb Re-processed data from Lynch et al. (2015)
P. antiquus_O O-NEU2A_merged_ReadGroups.bam/ O-NEU2A_merged_ReadGroups.bam.bai/ 0.6 Gb Data from Meyer et al. (2017)
M. primigenius_P P-Oimyakon_ReadGroups.bam/ P-Oimyakon_ReadGroups.bam.bai/ 41 Gb Re-processed data from Palkopoulou et al. (2015)
M. primigenius_Q Q-Wrangel_ReadGroups.bam/ Q-Wrangel_ReadGroups.bam.bai/ 40 Gb Re-processed data from Palkopoulou et al. (2015)
E. maximus_Y Y-Uno_loxAfr4com_v2_dedup.RG.bam/ Y-Uno_loxAfr4com_v2_dedup.RG.bam.bai/ 78 Gb Re-processed data from Lynch et al. (2015)
E. maximus_Z Z_SRR2912975.RG.bam / Z_SRR2912975.RG.bam.bai / 48 Gb Re-processed data from Reddy et al. (2015)


Note that all 7 bam files may be downloaded using the linux command: "wget -m http://reichdata.hms.harvard.edu/pub/datasets/probosc/bams/". You may also use this for individual filenames (or a set) using the bam names in the table above if you wish.

(Z) References

 Palkopoulou et al, 2018: Palkopoulou, et al. (2018) A comprehensive genomic history of extinct and living elephants. PNAS.
Lynch et al, 2015: Lynch Vincent J, et al. (2015) Elephantid Genomes Reveal the Molecular Bases of Woolly Mammoth Adaptations to the Arctic. Cell Reports 12(2):217-228.
Meyer et al, 2017: Meyer M, et al. (2017) Palaeogenomes of Eurasian straight-tusked elephants challenge the current view of elephant evolution. eLife 6:e25413.
Palkopoulou et al. 2015: Palkopoulou E, et al. (2015) Complete Genomes Reveal Signatures of Demographic and Genetic Declines in the Woolly Mammoth. Current Biology (25):1-6.
Reddy et al, 2015: Reddy PC, et al. (2015) Comparative sequence analyses of genome and transcriptome reveal novel transcripts and variants in the Asian elephant Elephas maximus. Journal of Biosciences 40(5):891-907.