Convergence among cave catfishes: long-branch attraction and a Bayesian relative rates test

Wilcox, Thomas P.; León, Francisco J. Garcı́a de; Hendrickson, Dean A.; Hillis, David M.

doi:10.1016/j.ympev.2003.11.006

Cited by 68 publications

(64 citation statements)

References 34 publications

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“…Despite the representation of distant taxa in the present study, we did not face a long-branch attraction problem as has been described in some other diverse groups (Wilcox et al 2004). The outgroup taxon, Cypriniformes, belonging to ray-finned fishes of the class Actinopterygii, formed phylogenetic clusters related to the Perciformes (Fig.…”

Section: Discussionmentioning

confidence: 47%

Molecular phylogenetics of pricklebacks and other percoid fishes from the Sea of Japan

Kartavtsev¹,

Sharina²,

Goto³

et al. 2009

Aquat. Biol.

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Mitochondrial DNA of the Co-1 gene region was sequenced for 8 fish species (in total 17 sequences of at least 532 bp) from the far east of Russia and compared to 3 other perciform sequences, altogether comprising 20 perch-like fish sequences and 2 outgroup sequences (Cypriniformes). The analysis of the protein-coding Co-1 gene revealed a statistically substantiated bias in the (T+C):(A+G) content, confirming the basic findings on the pyrimidines-prunes ratio. The average scores of p-distances for different scales of the evolutionary history of the Co-1 gene revealed a pattern of increased nucleotide diversity at 4 different levels: (1) intraspecies, (2) intragenus, (3) intrafamily and (4) intraorder. The scores of the average p-distances of the 4 categories of comparison were: (1) 0.11 ± 0.04%, (2) 1.87 ± 0.68%, (3) 12.67 ± 0.28%, and (4) 16.52 ± 0.10%, respectively (mean ± SE). These data support the concept that speciation in the order Perciformes in most cases follows a geographic mode through accumulation of numerous small genetic changes over a long time. The phylogenetic trees for 18 and 21 sequences of perch-like fishes together with 2 other fishes belonging to the ray-finned fishes (Actinopterygii) were developed using the Co-1 gene and 4 different analytical approaches: neighbour-joining (NJ), maximum likelihood (ML), Bayesian (BA) and maximum parsimony (MP). The analysis revealed a monophyletic origin for the representatives of the Stichaeidae, which was the principal percoid family investigated (86, 96 and 100% support in our NJ, ML and BA analyses, respectively). Species identification on a per individual basis or Co-1-based DNA barcoding was high.

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Section: Discussionmentioning

confidence: 47%

Molecular phylogenetics of pricklebacks and other percoid fishes from the Sea of Japan

Kartavtsev¹,

Sharina²,

Goto³

et al. 2009

Aquat. Biol.

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“…We used Bayesian relative rate tests (57) to test for constancy of evolutionary rates among plethodontids, and to test whether the differences are associated with any major clado-genetic or biogeographic events. To estimate divergence times among clades, we used a relaxed molecular clock Bayesian approach implemented in the package MULTIDIVTIME (20).…”

Section: Methodsmentioning

confidence: 99%

Rapid diversification and dispersal during periods of global warming by plethodontid salamanders

Vieites

Min

Wake

2007

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

207

235

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A phylogeny and timescale derived from analyses of multilocus nuclear DNA sequences for Holarctic genera of plethodontid salamanders reveal them to be an old radiation whose common ancestor diverged from sister taxa in the late Jurassic and underwent rapid diversification during the late Cretaceous. A North American origin of plethodontids was followed by a continentalwide diversification, not necessarily centered only in the Appalachian region. The colonization of Eurasia by plethodontids most likely occurred once, by dispersal during the late Cretaceous. Subsequent diversification in Asia led to the origin of Hydromantes and Karsenia, with the former then dispersing both to Europe and back to North America. Salamanders underwent rapid episodes of diversification and dispersal that coincided with major global warming events during the late Cretaceous and again during the Paleocene-Eocene thermal optimum. The major clades of plethodontids were established during these episodes, contemporaneously with similar phenomena in angiosperms, arthropods, birds, and mammals. Periods of global warming may have promoted diversification and both inter-and transcontinental dispersal in northern hemisphere salamanders by making available terrain that shortened dispersal routes and offered new opportunities for adaptive and vicariant evolution.historical biogeography ͉ paleogeography ͉ Plethodontidae dispersal ͉ salamander phylogeny ͉ phylogeny P lethodontidae, the most speciose family of salamanders, is also the most differentiated in morphology, ecology, and behavior. The family includes Ϸ68% of the extant described species of caudate amphibians (1). New analyses of mtDNA, nuclear DNA, and morphology (2-6) have achieved consensus on many aspects of phylogenetic relationships, but unresolved conflicts remain. The disjunct and highly asymmetric Holarctic distribution of the family, with Ϸ98% of the species in the Americas and a few in the Mediterranean region, has long been a biogeographic puzzle (7-9), with the debate centered on the timing and route of colonization of Eurasia (reinvigorated with the recent discovery of Karsenia, the first East Asian plethodontid; ref. 10

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“…To compare the substitution rate for each species, distances from the most recent common ancestor (MRCA) were estimated for each sampled tree in the BI analysis. The distance from the MRCA to each of the terminal taxa was calculated using Cadence v.1 (Wilcox et al 2004).…”

Section: Samplesmentioning

confidence: 99%

Phylogenetic position of Oxygyne shinzatoi (Burmanniaceae) inferred from 18S rDNA sequences

et al. 2007

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The genus Oxygyne comprises three species disjunctly distributed in Africa and Japan and is the least examined genus of the Burmanniaceae due to the scarcity of living material. We obtained living samples of Oxygyne shinzatoi and examined the phylogenetic position of this species on the basis on the 18S rDNA sequence. Oxygne shinzatoi was consistently found to belong to the monophyletic group of tribe Thismieae, but its position in the tribe differed depending on the criteria applied (maximum parsimony, maximum likelihood, Bayesian inference). Distance analysis from the most recent common ancestor indicated that O. shinzatoi had the lowest substitution rate among the species of tribe Thismieae. Combined with recent knowledge of basic chromosome numbers and substitution rate characteristics, O. shinzatoi can be considered to be one of the basal taxon of tribe Thismieae.

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Convergence among cave catfishes: long-branch attraction and a Bayesian relative rates test

Cited by 68 publications

References 34 publications

Molecular phylogenetics of pricklebacks and other percoid fishes from the Sea of Japan

Molecular phylogenetics of pricklebacks and other percoid fishes from the Sea of Japan

Rapid diversification and dispersal during periods of global warming by plethodontid salamanders

Phylogenetic position of Oxygyne shinzatoi (Burmanniaceae) inferred from 18S rDNA sequences

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