DOI: 10.5061/dryad.s1m9h
title: Data from: Splitting an ancient icon: mummy DNA resurrects a cryptic Nile crocodile

description: The Nile crocodile (Crocodylus niloticus) is an ancient icon of both
 cultural and scientific interest. The species is emblematic of the great
 civilizations of the Nile River valley and serves as a model for
 international wildlife conservation. Despite its familiarity, a
 centuries-long dispute over the taxonomic status of the Nile crocodile
 remains unresolved. This dispute not only confounds our understanding of
 the origins and biogeography of the “true crocodiles” of the crown genus
 Crocodylus, but also complicates conservation and management of this
 commercially valuable species. We have taken a total evidence approach
 involving phylogenetic analysis of mitochondrial and nuclear markers as
 well as karyotype analysis of chromosome number and structure to assess
 the monophyletic status of the Nile crocodile. Samples were collected from
 throughout Africa, covering all major bioregions. We also utilized
 specimens from museum collections, including mummified crocodiles from the
 ancient Egyptian temples at Thebes and the Grottes de Samoun, to
 reconstruct the genetic profiles of extirpated populations. Our analyses
 reveal a cryptic evolutionary lineage within the Nile crocodile that
 elucidates the biogeographic history of the genus and clarifies
 long-standing arguments over the species’ taxonomic identity and
 conservation status. An examination of crocodile mummy haplotypes
 indicates that the cryptic lineage corresponds to an earlier description
 of C. suchus and suggests that both African Crocodylus lineages
 historically inhabited the Nile River. Recent survey efforts indicate that
 C. suchus is declining or extirpated throughout much of its distribution.
 Without proper recognition of this cryptic species, current sustainable
 use-based management policies for the Nile crocodile may do more harm than
 good.
description: Hekkalaetal_MolEcol_2011_12sNexus file containing sequence data for the 12S rRNA mitochondrial gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.Hekkalaetal_MolEcol_2011_16sNexus file containing sequence data for the 16S rRNA mitochondrial gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.Hekkalaetal_MolEcol_2011_dloopNexus file containing sequence data for the control region/dloop mitochondrial gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.Hekkalaetal_MolEcol_2011_ND4Nexus file containing sequence data for the NADH dehydrogenase subunit 4 mitochondrial gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.Hekkalaetal_MolEcol_2011_wancyNexus file containing sequence data for the WANCY tRNA cluster from the ND2-flanking region including tRNA_Trp, tRNA_Ala, tRNA_Asn, tRNA_Cys, and part of tRNA_Tyr mitochondrial gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.Hekkalaetal_MolEcol_2011_rag1Nexus file containing sequence data for the rag-1 recombination activating gene-1 nuclear gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.Hekkalaetal_MolEcol_2011_S6Nexus file containing sequence data for the ribosomal protein S6 nuclear gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.Hekkalaetal_MolEcol_2011_TropNexus file containing sequence data for the tropomyosin intron nuclear gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.Hekkalaetal_MolEcol_2011_ODNexus file containing sequence data for the ornithine decarboxylase intron nuclear gene region. Please refer to Table 2 of the associated manuscript, as well as the Methods section, for specimen information.Hekkalaetal_MolEcol_2011_12s_museumdataONLYNexus file containing sequence data for the 12s rRNA mitochondrial gene region. Sequences listed here are the "short 12s" sequences for the museum and mummy specimens only. Please refer to the associated manuscript Table 2, and Methods, for further specimen information.Hekkalaetal_MolEcol_2011_dloop_museumdataONLYNexus file containing sequence data for the control region/dloop mitochondrial gene region. Sequences listed here are the "short dloop" sequences for the museum and mummy specimens only. Please refer to the associated manuscript Table 2, and Methods, for further specimen information.