Re: Homology in Phylogenetic Analysis: Alignment of Transfer RNA Genes and the Phylogenetic Position of Snakes

Macey,; Verma, AK

doi:10.1006/mpev.1997.0379

Cited by 71 publications

(43 citation statements)

References 9 publications

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“…DNA sequences were aligned in ClustalX 1.83 (Thompson et al, 1997) with default gap costs. Sequences encoding tRNAs were aligned by inferring secondary structures from primary structures of the corresponding tRNA genes based on standard tRNA models (Kumazawa and Nishida, 1993;Macey and Verma, 1997). Protein-coding sequences (i.e., ND1, ND2, COI, BDNF, RAG1) were translated into amino acids using MacClade 4.03 (Maddison and Maddison, 2001) for confirmation of alignment.…”

Section: Alignment Protocolsmentioning

confidence: 99%

Phylogeny of hoplocercine lizards (Squamata: Iguania) with estimates of relative divergence times

Torres‐Carvajal

Queiroz

2009

Molecular Phylogenetics and Evolution

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Section: Alignment Protocolsmentioning

confidence: 99%

Phylogeny of hoplocercine lizards (Squamata: Iguania) with estimates of relative divergence times

Torres‐Carvajal

Queiroz

2009

Molecular Phylogenetics and Evolution

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“…Positions encoding proteins were translated to amino acids using MacClade 4.03 (Maddison and Maddison, 2001) for confirmation of alignment. Alignments of sequences encoding tRNAs were constructed based on secondary structural models (Kumazawa and Nishida, 1993;Macey and Verma, 1997). Secondary structures of tRNAs were inferred from primary structures of the corresponding tRNA genes using these models.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genomic sequences

Macey

Papenfuss

Kuehl

et al. 2004

Molecular Phylogenetics and Evolution

106

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Key Words: Reptilia; Amphisbaenia; Bipes; phylogeny; mitochondrial DNA; genomics; limb evolution; biogeography; Pangaea. 3 INTRODUCTIONAmphisbaenians are fossorial reptiles that inhabit tropical and semitropical regions of the world (Fig. 1). The vast majority of species occur on land masses of Gondwanan origin in South America, Africa and Arabia. However, two of the four families are restricted to regions associated with Laurasia, the Bipedidae, with three species in Mexico (Fig. 2), and the Rhineuridae, with a single species in Florida. These taxa have pleurodont dentition (Gans, 1968) and were originally placed in the family Amphisbaenidae which now primarily includes taxa distributed in Gondwanan regions of South America and Africa (Gans, 1978). The fourth family of Amphisbaenia, the Trogonophidae, is the only one to have acrodont dentition and is restricted to Gondwanan plates of North Africa, Arabia and the island of Socotra. By superimposing a phylogeny of these groups on their distribution relative to the breakup of these major land masses, it is possible to test hypotheses about their origins. For example, monophyly of taxa found in Laurasia or Gondwana may reflect their isolation stemming from the breakup of Pangaea 200 million years before present (MYBP), (Fig. 3C, D).A phylogeny of Amphisbaenia is also important for reconstructing patterns of morphological change. Among the four families of Amphisbaenia, all taxa are limbless except the Bipedidae, which contains reptiles with two forelimbs. If gradual reduction in limbs were to have occurred from an ancestor with both hind and forelimbs, then the Bipedidae, with its presumed intermediate state, would be thought to be the sister taxon to the remaining families as has been suggested by morphological data (Kearney, 2003; Fig. 3B).Within the Bipedidae, species are variable for the number of digits on a limb (Papenfuss, 1982). The Baja California taxon, Bipes biporus, always has five digits on each limb. In mainland Mexico, the more northern taxon, B. canaliculatus, is variable, with either four or five 4 digits, while the more southern species, B. tridactylus, always has three digits on each limb. If digits are being gradually lost from an ancestor with five digits then B. biporus is predicted to be the sister taxon to the other two species (Fig. 3E). This phylogenetic hypothesis is consistent with an initial splitting of Bipes by the separation of peninsular Baja California from the west coast of Mexico (12-14 MYBP;Ferrari, 1995), with the two mainland species later diverging.Alternatively, tectonic activity along the west coast of Mexico in the Cretaceous to Paleocene (Ferrari, 1995) may have isolated the more northern taxa, B. biporus and B. canaliculatus, from B. tridactylus to the south (Fig. 3F).Mitochondrial gene order is a highly robust phylogenetic character for reconstructing evolutionary relationships among animals (Boore, 1999;Boore and Brown 1998;Macey et al., 1997aMacey et al., , 2000. Although no character can be asserted to be completely ...

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“…Alignment of tRNA genes was based on secondary structural models (Kumazawa & Nishida 1993;Macey & Verma 1997). Secondary structures of tRNAs were inferred from primary structures of the corresponding tRNA genes using these models.…”

Section: Methodsmentioning

confidence: 99%

Molecular phylogenetic evidence for ancient divergence of lizard taxa on either side of Wallace's Line

Schulte

Melville

Larson

2003

Proc. R. Soc. Lond. B

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Wallace's Line, separating the terrestrial faunas of South East Asia from the Australia-New Guinea region, is the most prominent and well-studied biogeographical division in the world. Phylogenetically distinct subgroups of major animal and plant groups have been documented on either side of Wallace's Line since it was first proposed in 1859. Despite its importance, the temporal history of fragmentation across this line is virtually unknown and the geological foundation has rarely been discussed. Using molecular phylogenetics and dating techniques, we show that the split between taxa in the South East Asian and the Australian-New Guinean geological regions occurred during the Late Jurassic to Early Cretaceous in two independent lizard clades. This estimate is compatible with the hypothesis of rifting Gondwanan continental fragments during the Mesozoic and strongly rejects the hypothetical origin of various members of the Australian-New Guinean herpetofauna as relatively recent invasions from South East Asia. Our finding suggests an ancient fragmentation of lizard taxa on either side of Wallace's Line and provides further evidence that the composition of modern global communities has been significantly affected by rifting and accretion of Gondwanan continental plates during the Middle to Late Mesozoic.

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Re: Homology in Phylogenetic Analysis: Alignment of Transfer RNA Genes and the Phylogenetic Position of Snakes

Cited by 71 publications

References 9 publications

Phylogeny of hoplocercine lizards (Squamata: Iguania) with estimates of relative divergence times

Phylogeny of hoplocercine lizards (Squamata: Iguania) with estimates of relative divergence times

Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genomic sequences

Molecular phylogenetic evidence for ancient divergence of lizard taxa on either side of Wallace's Line

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