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Are Crocodiles Really Monophyletic?



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Molecular Phylogenetics and Evolution 39 2006 16 32 www elsevier com locate ympev Are crocodiles really monophyletic Evidence for subdivisions from sequence and morphological data L Rex McAliley a Ray E Willis a David A Ray a 1 P Scott White b Christopher A Brochu c Llewellyn D Densmore III a b a Department of Biological Sciences Texas Tech University P O Box 43131 Lubbock TX 79409 313 USA Genetic Variation Initiative MailStopM888 Bioscience Division Los Alamos National Laboratory Los Alamos NM 87545 USA c Department of Geoscience University of Iowa Iowa City IA 52242 USA Received 2 February 2005 revised 9 January 2006 accepted 10 January 2006 Available online 21 February 2006 Abstract Recently the phylogenetic placement of the African slender snouted crocodile Crocodylus cataphractus has come under scrutiny and herein we address this issue using molecular and morphological techniques Although it is often recognized as being a basal form morphological studies have traditionally placed C cataphractus within the genus Crocodylus while molecular studies have suggested that C cataphractus is very distinct from other Crocodylus To address the relationship of this species to its congeners we have sequenced portions of two nuclear genes C mos 302 bp and ODC 294 bp and two mitochondrial genes ND6 tRNAglu cytB 347 bp and control region 457 bp Analyses of these molecular datasets both as individual gene sequences and as concatenated sequences support the hypothesis that C cataphractus is not a member of Crocodylus or Osteolaemus Examination of 165 morphological characters supports and strengthens our resurrection of an historic genus Mecistops Gray 1844 for cataphractus 2006 Elsevier Inc All rights reserved Keywords Crocodylus Crocodylus cataphractus C mos ODC Mitochondrial ND6 Mitochondrial control region Systematics Mecistops 1 Introduction The African slender snouted crocodile Crocodylus cataphractus has long been a systematic enigma In one of the earliest systematic treatments of what is now called Crocodylia Gmelin 1789 indicated that the habitat for Lacerta gangeticus now Gavialis gangeticus included rivers in Senegal Africae et Gangen Indiae Gavialis has been restricted to the Indian subcontinent throughout historical times but it is clear from Gmelin s diagnosis that C cataphractus the crocodylian from Senegal with an elongate subcylindrical rostrum would have fallen within Corresponding author Fax 1 806 742 2369 E mail address rexmcaliley excite com L R McAliley 1 Present Address Department of Biology West Virginia University 53 Campus Dr Morgantown WV 26505 USA 1055 7903 see front matter 2006 Elsevier Inc All rights reserved doi 10 1016 j ympev 2006 01 012 L gangeticus highlighting the morphological gulf between C cataphractus and other Crocodylus reinforcing the need for further systematic analysis Various members of the genus Crocodylus the true crocodiles have been included in a number of phylogenetic studies but until recently very little had been written about relationships within Crocodylus That the name Crocodylus lacked a uniform meaning renders comparisons of diVerent scenarios virtually impossible Neontologists were necessarily restricted to the 12 recognized living species but paleontologists assigned fossils ranging throughout the Cenozoic and into the Mesozoic sometimes as old as the Albian stage of the Cretaceous between 99 and 112 mya to Crocodylus Markwick 1998 Steel 1973 Explicit diagnoses not reliant on overall head shape were rarely used and Crocodylus was often a default category that simply meant a fossil could not be unambiguously assigned to some other L R McAliley et al Molecular Phylogenetics and Evolution 39 2006 16 32 genus Several authors have suggested that the African slender snouted crocodile C cataphractus is the sister taxon to a clade comprising all other members of this genus Brochu 1997 2000 Densmore 1983 Densmore and Owen 1989 Gatesy et al 2003 Gatesy et al 2004 White and Densmore 2000 Most of these studies have suVered from limited taxon sampling and or few representative individuals from the species being compared To date there have been few studies aimed speciWcally at the relationship of this species to its congeners and no molecular studies Recently Schmitz et al 2003 in a study on genetic variation within the Nile crocodile C niloticus suggested that C cataphractus formed a relationship outside the remainder of Crocodylus However this portion of their study included just a single C cataphractus sample two dwarf African crocodile samples Osteolaemus tetraspis and only three of the eleven recognized extant species of Crocodylus C cataphractus C jonstoni and C niloticus Herein using more thorough taxon sampling and much larger sample sizes especially for the nuclear gene sequences we report sequence comparisons from both coding and non coding regions of two nuclear protein coding genes and from two diVerent regions of the mitochondrial genome also representing both coding and non coding sequences speciWcally to assess the relationship of C cataphractus to other members of Crocodylus and to Osteolaemus The two nuclear markers sequenced for this study are the proto oncogene C mos and the gene that codes for ornithine decarboxylase ODC C mos is a single copy gene slightly over 1000 bp in length contains no introns and codes for a protein C mos involved in oocyte maturation during meiotic metaphase II Saint et al 1998 Yew et al 1993 Due to its relative high degree of conservation this gene provided the resolution necessary to examine generic level relationships within the Crocodylia The ODC gene codes for a protein that catalyses the conversion of ornithine to putricine Friesen et al 1999 and is involved in the control of cell growth and division Yao et al 1995 Comprising some 12 exons and 11 introns it has a transcription unit 6 8 kb in length Friesen et al 1999 characterized a series of PCR primers for this gene spanning a region from intron 6 through intron 8 However they did not test the amplicons produced with these primers for phylogenetic signal While the use of the ODC gene in phylogenetic analyses has been limited it has been shown to be comparable to both mitochondrial cytochrome b Allen and Omland 2003 and control region Kulikova et al 2004 sequences at resolving phylogenetic relationships Mitochondrial sequence data continue to be widely used in many systematic studies including crocodylians Gatesy and Amato 1992 Gatesy et al 2003


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