Molecular phylogenetics and biogeography of galaxiid fishes (Osteichthyes: Galaxiidae): dispersal, vicariance, and the position of Lepidogalaxias salamandroides.
TL;DR: 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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TL;DR: Rejection of the null hypothesis for the majority of pairs implies that the extant New Zealand lineage has undergone long-distance dispersal either into or out of New Zealand, and the notion of a long isolation since geological separation can be dismissed for much of the pteridophyte flora.
Abstract: Aim To examine the relative importance of long-distance dispersal in shaping the New Zealand pteridophyte (ferns and lycophytes) flora and its relationships with other floras, with the null hypothesis that the extant New Zealand pteridophyte flora has been isolated since New Zealand’s separation from Gondwana.
Location New Zealand.
Methods rbcL DNA sequences were assembled for 31 New Zealand pteridophyte genera, with each genus represented by one New Zealand species and the most closely related non-New Zealand species for which data were available. Maximum-likelihood, maximum-parsimony, and Bayesian analysis phylograms were constructed and used as input for r8s molecular dating, along with 23 fossil calibrations. Divergence estimates less than conservatively recent ages for New Zealand’s geological isolation, namely Ho > 30 Ma for pairs involving New Caledonian and Norfolk Island species and Ho > 55 Ma for all others, were taken as rejection of the null hypothesis.
Results The null hypothesis was rejected for all pairs except, under some parameter conditions, for those involving the New Zealand species Cardiomanes reniforme, Lindsaea trichomanoides, Loxsoma cunninghamii, Lygodium articulatum, Marattia salicina, and Pteris comans. However, the Lindsaea and Pteris results probably reflect the absence in the analyses of closely related non-New Zealand samples, while the Marattia divergence was highly contingent on which fossil calibrations were used.
Main conclusions Rejection of the null hypothesis for the majority of pairs implies that the extant New Zealand lineage has undergone long-distance dispersal either into or out of New Zealand. The notion of a long isolation since geological separation can, therefore, be dismissed for much of New Zealand’s pteridophyte flora. The analyses do not identify the direction of the long-distance dispersal, and these New Zealand lineages could have had vicariant origins with subsequent long-distance emigration. However, the alternative that many extant New Zealand pteridophyte lineages only arrived by long-distance immigration after geological isolation seems likely.
64 citations
TL;DR: It is recommended that morphological systematists routinely implement a range of character transformation models to assess the sensitivity of their phylogenetic reconstructions, and it is proposed that a simple "equal transformation cost" parsimony analysis may be biologically unrealistic.
Abstract: WeusedmitochondrialDNAsequencestodeterminethephylogeneticplacementofsouth- ern smelts (Retropinnidae), a group of diadromous eshes endemic to New Zealand and Australia. Our genetic data strongly support a sister group relationship between retropinnids and northern hemisphere smelts (Osmeridae), a relationship that seems consistent with the similar appearance and life history strategies of these two groups. Our analysis indicates that Retropinnidae and Osmeridae together represent the sister group to the southern hemisphere galaxiid eshes (Galaxiidae). However, this ending coneicts with several recent osteological analyses, which supported a sister relationship for Retropinnidae and Galaxiidae, giving a monophyletic southern hemisphere assemblage (Galax- ioidea). We review cases of incongruence and discuss factors that might explain signiecant disagree- ment between molecular and morphological data matrices. We suggest that repeated evolutionary simpliecation may haveundermined the accuracy of morphologicalhypotheses of osmeroid relation- ships. Although equally weighted parsimony analysis of morphological data rejects the molecular hypothesis (Osmeridae C Retropinnidae), implementation of a range of weighting schemes suggests that incongruence is nonsigniecant under asymmetric character transformation models. We propose that a simple "equal transformation cost" parsimony analysis may be biologically unrealistic, espe- cially when reductive homoplasy is widespread; as is increasingly being accepted, complex character states are more readily lost than gained. Therefore, we recommend that morphological systematists routinely implement arange of character transformation models to assess the sensitivity of their phy- logenetic reconstructions. We discuss the antitropical biogeography of osmeroid eshes in the context of vicariance and transequatorial dispersal. (16S; Australia; character transformation; congruence; cyt b; galaxiid; New Zealand; osmerid; retropinnid; smelt.)
56 citations
TL;DR: What appears to be a multi-era tangle of convoluted, trans-oceanic distributions on Panthalassa-based paleomaps is actually a relatively simple biogeographical pattern that is explainable by a single vicariant event: the opening and expansion of the Pacific.
Abstract: Aim To combine analyses of trans-Pacific sister taxa with geological evidence in order to test the hypothesis of the existence of a Panthalassa superocean.
Location The study is concerned with taxa, both fossil and extant, from East Asia, Australia, New Zealand, South America and North America.
Methods Phylogenetic and distributional analyses of trans-Pacific biota were integrated with geological evidence from the Pacific and circum-Pacific regions.
Results A series of recent biogeographical analyses delineates a zipper-like system of sister areas running up both margins of the Pacific, with each section of western North and South America corresponding to a particular section from East Asia/Australia/New Zealand. These sister areas coincide neatly with a jigsaw-like fit provided by the matching Mesozoic coastlines that bracket the Pacific.
Main conclusions The young age (<200 Myr) of oceanic crust, the matching Mesozoic circum-Pacific outlines, and a corresponding system of interlocking biogeographical sister areas provide three independent avenues of support for a closed Pacific in the Upper Triassic–Lower Jurassic. The hypothesis of the existence and subsequent subduction of the pre-Pacific superocean Panthalassa is not only unnecessary, it conflicts with this evidence. Panthalassa-based paleomaps necessitate the invention of dozens of additional hypotheses of species-dependent, trans-oceanic dispersal events, often involving narrow-range taxa of notoriously limited vagility, in order to explain repeated examples of the same biogeographical pattern. Removing the vanished-superocean hypothesis reunites both the matching geological outlines and all the disjunct sister taxa. In brief, what appears to be a multi-era tangle of convoluted, trans-oceanic distributions on Panthalassa-based paleomaps is actually a relatively simple biogeographical pattern that is explainable by a single vicariant event: the opening and expansion of the Pacific.
56 citations
Cites background from "Molecular phylogenetics and biogeog..."
...Waters et al. (2000), following plate tectonic paleomaps, had to invoke both trans-oceanic dispersal and trans-Antarctic migration and extinction to explain these distributions....
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...More recently, Waters et al. (2000) used mitochondrial DNA sequences to analyse biogeographical hypotheses for the trans-Southern Pacific distribution of galaxiid fishes....
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...As both the Australian and Chilean taxa are limited to freshwater (nonmigratory), Waters et al. (2000) felt that trans-Antarctic vicariance, rather than oceanic dispersal, was the most plausible explanation for this particular distribution, noting that the divergence might have occurred much…...
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...Similarly, in Chile it is found between 32 and 54 S (Berra et al., 1996; T.M. Berra, pers. comm.) Waters et al. (2000) suppose the 2003 Blackwell Publishing Ltd, Journal of Biogeography, 30, 1545–1561 distribution of Galaxias maculatus to be the result of transoceanic dispersal....
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...Waters et al. (2000) wrote: Given the strong morphological similarities and the mtDNA support (albeit weak) for their monophyly, we recommend that the Australian species be restored to Brachygalaxias, with Galaxiella used for subgeneric ranking if necessary ....
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TL;DR: The results suggest that Lepidogalaxias occupies a basal position among all euteleosts, in contrast with earlier hypotheses that variously suggested a closer relationship to esocid fishes, or to the galaxiid Lovettia.
55 citations
Cites background from "Molecular phylogenetics and biogeog..."
...Detailed analyses of molecular data based on intensive taxa sampling by Waters et al. (2000, 2002) of galaxiids, which Nelson (2006) placed within Osmeriformes, represent a monophyletic group that is the sister group of other orders together (Argentiniformes, Esociformes, Salmoniformes,…...
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...Waters et al. (2000) ll rights reserved. concluded that Lepidogalaxias is not a galaxiid based on mitochondrial DNA sequences, but again, Waters et al.’s (2000) study was based on a limited diversity of fish genera....
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...The first molecular study of relationships of Lepidogalaxias was by Waters et al. (2000)....
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TL;DR: In this article, the authors define three environmental indicators, which are detectable as concordant patterns in the geological and fossil records: freshwater radiations, vicariant events and sea temperature, and mapped the indicators onto a phylogeny of the Late Jurassic-Palaeocene actinopterygian taxa and plotted the variations against time for each of the indicators.
51 citations
Cites background from "Molecular phylogenetics and biogeog..."
...A recent example of such dispersal was described in the galaxiids (Waters et al., 2000)....
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References
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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.
Abstract: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.
63,427 citations
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.
Abstract: The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
40,349 citations
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.
Abstract: Some simple formulae were obtained which enable us to estimate evolutionary distances in terms of the number of nucleotide substitutions (and, also, the evolutionary rates when the divergence times are known). In comparing a pair of nucleotide sequences, we distinguish two types of differences; if homologous sites are occupied by different nucleotide bases but both are purines or both pyrimidines, the difference is called type I (or “transition” type), while, if one of the two is a purine and the other is a pyrimidine, the difference is called type II (or “transversion” type). Letting P and Q be respectively the fractions of nucleotide sites showing type I and type II differences between two sequences compared, then the evolutionary distance per site is K = — (1/2) ln {(1 — 2P — Q) }. The evolutionary rate per year is then given by k = K/(2T), where T is the time since the divergence of the two sequences. If only the third codon positions are compared, the synonymous component of the evolutionary base substitutions per site is estimated by K'S = — (1/2) ln (1 — 2P — Q). Also, formulae for standard errors were obtained. 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.
26,016 citations
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.
Abstract: The application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed. A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available. This method has advantages over the traditional parsimony algorithms, which can give misleading results if rates of evolution differ in different lineages. It also allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests, and gives rough indication of the error of the estimate of the tree.
13,111 citations
01 Jan 1969
10,262 citations