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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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Do insects lose flight before they lose their wings? Population genetic structure in subalpine stoneflies.

TL;DR: Intriguingly, the variable degrees of wing development observed within the fenestrata species group had no apparent impact on levels of phylogeographic structure, suggesting that even fully winged specimens of this group do not fly.
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Process and pattern in the biogeography of New Zealand – a global microcosm?

TL;DR: New Zealand’s historical terrestrial biogeography is described to place this history in a wider Southern Hemisphere context.
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Surviving historical Patagonian landscapes and climate: molecular insights from Galaxias maculatus

TL;DR: The minor influence of glacial cycles on the genetic structure and diversity of G. maculatus likely reflects the access to marine refugia during repeated bouts of global cooling and the Coastal Cordillera as a dispersal barrier.
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Gene Trees versus Species Trees: Reassessing Life-History Evolution in a Freshwater Fish Radiation

TL;DR: A variety of nuclear DNA loci are employed to reassess evolutionary relationships within a recent freshwater fish radiation to reappraise modes of speciation and discuss factors that might explain the apparently misleading phylogenetic inferences generated by mtDNA.
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Geological Dates and Molecular Rates: Rapid Divergence of Rivers and Their Biotas

TL;DR: A survey of freshwater phylogeographic literature reveals numerous examples in which the ages of recent evolutionary events may have been substantially overestimated through the use of "accepted" calibrations, and recommends thatbiologists should start to reassess the conclusions of such studies by using more appropriate molecular calibrations derived from recent geological events.
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.