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.
Hekkalaetal_MolEcol_2011_12s
Nexus 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_16s
Nexus 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_dloop
Nexus 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_ND4
Nexus 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_wancy
Nexus 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_rag1
Nexus 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_S6
Nexus 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_Trop
Nexus 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_OD
Nexus 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_museumdataONLY
Nexus 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_museumdataONLY
Nexus 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.