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Molecular phylogenetics and biogeography of galaxiid fishes (Osteichthyes: Galaxiidae): dispersal, vicariance, and the position of Lepidogalaxias salamandroides.

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TLDR
The species-rich genus Galaxias is shown to be polyphyletic and the generic taxonomy of the Galaxiinae is reassessed in the light of phylogenetic relationships, and the loss of this migratory phase may be a major cause of speciation.
Abstract
The galaxiid fishes exhibit a gondwanan distribution. We use mitochondrial DNA sequences to test conflicting vicariant and dispersal biogeographic hypotheses regarding the Southern Hemisphere range of this freshwater group. Although phylogenetic resolution of cytochrome b and 16S rRNA sequences is largely limited to more recent divergences, our data indicate that the radiation can be interpreted as several relatively recent dispersal events superimposed on an ancient gondwanan radiation. Genetic relationships contradict the findings of recent morphological analyses of galaxioid fishes. In particular, we examine several hypotheses regarding phylogenetic placement of the enigmatic Lepidogalaxias. Although most workers consider Lepidogalaxias to be an unusual scaled member of the Southern Hemisphere galaxioids, it has also been suggested that this species is related to the Northern Hemisphere esocoids. Our data strongly suggest that this species is not a galaxiid, and the alternative hypothesized esocoid relationship cannot be rejected. The species-rich genus Galaxias is shown to be polyphyletic and the generic taxonomy of the Galaxiinae is reassessed in the light of phylogenetic relationships. Juvenile saltwater-tolerance is phylogenetically distributed throughout the Galaxiinae, and the loss of this migratory phase may be a major cause of speciation.

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Genes meet geology: fish phylogeographic pattern reflects ancient, rather than modern, drainage connections

TL;DR: DNA analysis of the freshwater Galaxias vulgaris complex was used to test a geological hypothesis of drainage evolution in South Island, New Zealand, and indicated that the Nevis flow reversal may have occurred in the early‐mid Pleistocene, which is roughly consistent with geological data.
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Directional asymmetry of long-distance dispersal and colonization could mislead reconstructions of biogeography

TL;DR: The authors discuss shortcomings in most current tree-based biogeography interpretation methods and show that consideration of processes and their likelihoods can turn the conventional biogeographical interpretation on its head.
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A molecular phylogeny of the Littorininae (Gastropoda: Littorinidae): unequal evolutionary rates, morphological parallelism, and biogeography of the Southern Ocean

TL;DR: The molecular phylogeny provides a new framework for the adaptive radiation of the Littorininae, showing more frequent shifts between habitats and climatic regimes than previously suspected, and striking parallelism of morphological characters.
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Biogeography of a southern hemisphere freshwater fish: how important is marine dispersal?

TL;DR: Phylogeographic analyses of 163 control region haplotypes of G. maculatus indicate that inter‐continental marine dispersal occurs but is insufficient to prevent mitochondrial DNA differentiation among continents, and the sister relationship of Tasmanian and New Zealand clades implies that marine disperseal is an important biogeographical mechanism for this species.

Hello New Zealand

TL;DR: In terms of evolution on Pacific islands, Cowie and Holland as discussed by the authors set New Zealand apart, as many have done before, as being continental, the implication being that the evolution of New Zealand biota is somehow subject to different processes from those of oceanic islands.
References
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Journal ArticleDOI

Clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

TL;DR: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available.
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Confidence limits on phylogenies: an approach using the bootstrap.

TL;DR: The recently‐developed statistical method known as the “bootstrap” can be used to place confidence intervals on phylogenies and shows significant evidence for a group if it is defined by three or more characters.
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A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.

TL;DR: Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.
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Evolutionary trees from DNA sequences: A maximum likelihood approach

TL;DR: A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available that allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests.