True and False Gharials: A Nuclear Gene Phylogeny of Crocodylia

Harshman, John; Huddleston, Christopher J.; Bollback, Jonathan P.; Parsons, Thomas J.; Braun, Michael J.

doi:10.1080/10635150309323

Cited by 31 publications

(54 citation statements)

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“…The disagreement between the morphological and the molecular results can, however, in essence be reduced to the placement of the root of the crocodilian tree. Morphological data have in general placed it on Gavialis (Norell 1989;Brochu 1997;Poe 1996), while the mitogenomic analysis and other molecular data (Densmore 1983;Gatesy et al 1993Gatesy et al , 2003Hass et al 1992;Harshman et al 2003) place it on the branch that separates the Alligatoridae.…”

Section: Discussionmentioning

confidence: 99%

“…The study by Harshman et al (2003) was based on a part of the cmyc nuclear gene, while that by Gatesy et al (2003) used a combination of the RAG-1 nuclear sequence plus about 800 nt from portions of the mt 12S rRNA, 16S rRNA, and cytochrome b genes. The nuclear sequences joined Gavialis and Tomistoma but the position of the branch was not conclusively settled.…”

Section: Introductionmentioning

confidence: 99%

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Mitogenomic Analyses Place the Gharial (Gavialis gangeticus) on the Crocodile Tree and Provide Pre-K/T Divergence Times for Most Crocodilians

et al. 2005

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Abstract. Based on morphological analyses, extant members of the order Crocodylia are divided into three families, Alligatoridae, Crocodylidae, and Gavialidae. Gavialidae includes one species, the gharial, Gavialis gangeticus. In this study we have examined crocodilian relationships in phylogenetic analyses of seven mitochondrial genomes that have been sequenced in their entirety. The analyses did not support the morphologically acknowledged separate position of the gharial in the crocodilian tree. Instead the gharial joined the false gharial (Tomistoma schlegelii) on a common branch that was shown to constitute a sister group to traditional Crocodylidae (less Tomistoma). Thus, the analyses suggest the recognition of only two Crocodylia families, Alligatoridae and Crocodylidae, with the latter encompassing traditional Crocodylidae plus Gavialis/Tomistoma. A molecular dating of the divergence between Alligatoridae and Crocodylidae suggests that this basal split among recent crocodilians took place 140 million years before present, at the Jurassic/Cretaceous boundary. The results suggest that at least five crocodilian lineages survived the mass extinction at the KT boundary.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Mitogenomic Analyses Place the Gharial (Gavialis gangeticus) on the Crocodile Tree and Provide Pre-K/T Divergence Times for Most Crocodilians

et al. 2005

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“…Although the traditional view is that the root lies between paleognath and neognath clades (12,27,46), early analyses of mtDNA placed the root either between passerines and all other birds (47) or within passerines (48,49), contradicting neognath monophyly. More sophisticated analyses (e.g., RY-coding) of mtDNA data strongly support the traditional rooting (22,23,50,51), unlike the early analyses.…”

Section: Monophyly Of Australasian Ratites Placement Of Tinamous Anmentioning

confidence: 99%

“…We assembled a dataset of 20 nuclear loci widely dispersed in the avian genome [supporting information (SI) Table S1] to examine ratite monophyly. It contains Ϸ30% protein-coding and 70% noncoding sequence (Table S1), taking advantage of the phylogenetic signal in archosaur noncoding sequences (26)(27)(28). The dataset comprises 18 taxa, including all extant ratite genera, four tinamou genera, and eight outgroup taxa (Table S2).…”

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confidence: 99%

Phylogenomic evidence for multiple losses of flight in ratite birds

Harshman

Braun

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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194

227

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Ratites (ostriches, emus, rheas, cassowaries, and kiwis) are large, flightless birds that have long fascinated biologists. Their current distribution on isolated southern land masses is believed to reflect the breakup of the paleocontinent of Gondwana. The prevailing view is that ratites are monophyletic, with the flighted tinamous as their sister group, suggesting a single loss of flight in the common ancestry of ratites. However, phylogenetic analyses of 20 unlinked nuclear genes reveal a genome-wide signal that unequivocally places tinamous within ratites, making ratites polyphyletic and suggesting multiple losses of flight. Phenomena that can mislead phylogenetic analyses, including long branch attraction, base compositional bias, discordance between gene trees and species trees, and sequence alignment errors, have been eliminated as explanations for this result. The most plausible hypothesis requires at least three losses of flight and explains the many morphological and behavioral similarities among ratites by parallel or convergent evolution. Finally, this phylogeny demands fundamental reconsideration of proposals that relate ratite evolution to continental drift.convergence ͉ flightlessness ͉ Paleognath ͉ homoplasy ͉ vicariance biogeography

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“…The c-myc gene mutations resulted in the reduced individual size, and tumor [23] had already been proved to occur in animals. Recently, the c-myc gene was used to infer phylogeny in mammals [24] , avians [25] , crocodiles [26] , and frogs [27] , and served as a useful molecular marker to investigate the higher-level phylogenies such as order and family. However, as far as we know, phylogenetic studies of fishes based on the c-myc gene have not been available.…”

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confidence: 99%

The c-myc coding DNA sequences of cyprinids (Teleostei: Cypriniformes): Implications for phylogeny

et al. 2007

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The family Cyprinidae is one of the largest fish families in the world, which is widely distributed in East Asian, with obvious difference in characteristic size among species. The phylogenetic analysis of cyprinid taxa based on the functionally important genes can help to understand the speciation and functional divergence of the Cyprinidae. The c-myc gene is an important gene regulating individual growth. In the present study, the sequence variations of the cyprinid c-myc gene and their phylogenetic significance were analyzed. The 41 complete sequences of the c-myc gene were obtained from cyprinids and outgroups through PCR amplification and clone. The coding DNA sequences of the c-myc gene were used to infer molecular phylogenetic relationships within the Cyprinidae. Myxocyprinus asiaticus (Catostomidae), Misgurnus anguillicaudatus (Cobitidae) and Hemimyzon sinensis (Homalopteridae) were assigned to the outgroup taxa. Phylogenetic analyses using maximum parsimony (MP), maximum likelihood (ML), and Bayesian retrieved similar topology. Within the Cyprinidae, Leuciscini and Barbini formed the monophyletic lineage respectively with high nodal supports. Leuciscini comprises Xenocyprinae, Cultrinae, East Asian species of Leuciscinae and Danioninae, Gobioninae and Acheilognathinae, and Barbini contains Schizothoracinae, Barbinae, Cyprininae and Labeoninae. Danio rerio, D. myersi and Rasbora trilineata were supposed to separate from Leuciscinae and Barbini and to form another lineage. The positions of some Danioninae species were still unresolved. Analyses of both amino acid variation with parsimony information and two high variation regions indicated that there is no correlation between variations of single amino acid or high variation regions and characteristic size of cyprinids. In addition, the species with smaller size were usually found to be basal within clades in the tree, which might be the results of the adaptation to the primitive ecology and survival pressure.

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True and False Gharials: A Nuclear Gene Phylogeny of Crocodylia

Cited by 31 publications

References 0 publications

Mitogenomic Analyses Place the Gharial (Gavialis gangeticus) on the Crocodile Tree and Provide Pre-K/T Divergence Times for Most Crocodilians

Mitogenomic Analyses Place the Gharial (Gavialis gangeticus) on the Crocodile Tree and Provide Pre-K/T Divergence Times for Most Crocodilians

Phylogenomic evidence for multiple losses of flight in ratite birds

The c-myc coding DNA sequences of cyprinids (Teleostei: Cypriniformes): Implications for phylogeny

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