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Zool."],"published-print":{"date-parts":[[2008,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>We analyzed DNA sequences of the mitochondrial cytochrome <jats:italic>b<\/jats:italic> gene (cyt <jats:italic>b<\/jats:italic>), the nuclear Recombination Activating Gene 1 (RAG1) and the myelocytomatosis oncogene (MYC) to infer the phylogenetic relationship of <jats:italic>Caiman crocodilus<\/jats:italic> and <jats:italic>Caiman yacare<\/jats:italic>, and other South American alligatorid crocodilian species. Phylogenetic relationships were robustly supported with <jats:italic>Paleosuchus<\/jats:italic> sister to <jats:italic>Melanosuchus<\/jats:italic> and <jats:italic>Caiman<\/jats:italic>. Phylogenetic relationships of <jats:italic>C. crocodilus<\/jats:italic> and <jats:italic>C. yacare<\/jats:italic> were unclear as these two species share mitochondrial and nuclear haplotypes. Specifically this sharing occurs among specimens of <jats:italic>C. yacare<\/jats:italic> and <jats:italic>C. crocodilus<\/jats:italic> from the Madeira River drainage. Two potential explanations stand out: secondary contact followed by hybridization, and differentiation along a cline. Current data cannot resolve between these two competing hypotheses. In comparison with <jats:italic>C. yacare<\/jats:italic> and <jats:italic>C. crocodilus<\/jats:italic>, <jats:italic>Paleosuchus trigonatus<\/jats:italic> and <jats:italic>Paleosuchus palpebrosus<\/jats:italic> are very well differentiated and also show surprising haplotypic diversity in spite of their phenotypic similarity. <jats:italic>J. Exp. Zool. 309A:588\u2013599, 2008<\/jats:italic>. \u00a9 2007 Wiley\u2010Liss, Inc.<\/jats:p>","DOI":"10.1002\/jez.430","type":"journal-article","created":{"date-parts":[[2007,12,27]],"date-time":"2007-12-27T19:19:35Z","timestamp":1198783175000},"page":"588-599","source":"Crossref","is-referenced-by-count":42,"title":["Phylogenetic relationships of South American Alligatorids and the <i>Caiman<\/i> of Madeira River"],"prefix":"10.1002","volume":"309A","author":[{"given":"Tomas","family":"Hrbek","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William Rangel","family":"Vasconcelos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George","family":"Rebelo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Izeni Pires","family":"Farias","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2007,12,27]]},"reference":[{"key":"e_1_2_1_2_1","volume-title":"Molecular markers, natural history and evolution","author":"Avise JC","year":"2004"},{"key":"e_1_2_1_3_1","doi-asserted-by":"publisher","DOI":"10.1163\/156853898X00476"},{"key":"e_1_2_1_4_1","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/46.3.479"},{"key":"e_1_2_1_5_1","first-page":"294","article-title":"Geographic variation in Caiman crocodilus and Caiman yacare (Crocodylia: Alligatoridae): systematics and legal implications","volume":"57","author":"Busack SD","year":"2001","journal-title":"Herpetologica"},{"key":"e_1_2_1_6_1","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-294x.2000.01020.x"},{"key":"e_1_2_1_7_1","doi-asserted-by":"publisher","DOI":"10.2307\/1446388"},{"key":"e_1_2_1_8_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.179.4070.243"},{"key":"e_1_2_1_9_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1558-5646.1985.tb00420.x"},{"key":"e_1_2_1_10_1","doi-asserted-by":"publisher","DOI":"10.1080\/10635150390197037"},{"key":"e_1_2_1_11_1","doi-asserted-by":"publisher","DOI":"10.1214\/ss\/1177011136"},{"key":"e_1_2_1_12_1","doi-asserted-by":"publisher","DOI":"10.1023\/A:1018320925954"},{"key":"e_1_2_1_13_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00299-001-0399-7"},{"key":"e_1_2_1_14_1","doi-asserted-by":"publisher","DOI":"10.1098\/rspb.2000.1385"},{"key":"e_1_2_1_15_1","doi-asserted-by":"publisher","DOI":"10.1080\/10635150390197028"},{"key":"e_1_2_1_16_1","doi-asserted-by":"publisher","DOI":"10.1016\/1055-7903(92)90015-9"},{"key":"e_1_2_1_17_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ympev.2006.06.009"},{"key":"e_1_2_1_18_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-2699.2006.01518.x"},{"key":"e_1_2_1_19_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/17.8.754"},{"key":"e_1_2_1_20_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1065889"},{"key":"e_1_2_1_21_1","volume-title":"Crocodilian, tuatara and turtle species of the world. 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