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: MP, ML and Bayesian analyses coupled with inclusion in analyses of GenBank-derived sequences of osmerid species that do not inhabit this region suggest that the lineage of the genus Mallotus was the first to separate from the common hypothetic ancestor of the smelts and is sister to the Osmerus–Hypomesus clade.
Abstract: Relationships of seven species of smelts (family Osmeridae) inhabiting Russian waters were analyzed on the basis of nucleotide sequence divergence of cytb, COI and intron 1 of rpS7 genes. Nuclear sequence divergence between the species within of the genera Osmerus, Mallotus and Hypomesus was 1.6–2.6, 2.9 and 6.6–11.8 %, respectively, and mitochondrial sequence divergence was 8.9–9.7, 3.9 and 15.1–18.3 %, respectively. The mtDNA divergence was 20.4 % between the genera Hypomesus and Mallotus, 18.47 % between Hypomesus and Osmerus, and 17.62 % between Mallotus and Osmerus. Nuclear DNA divergence was 11.58, 11.19, and 11.37 %, respectively. MP, ML and Bayesian analyses coupled with inclusion in analyses of GenBank-derived sequences of osmerid species that do not inhabit this region suggest that the lineage of the genus Mallotus was the first to separate from the common hypothetic ancestor of the smelts and is sister to the Osmerus–Hypomesus clade. The position of Hypomesus olidus is not resolved and points to the need for further research.
13 citations
Cites background from "Molecular phylogenetics and biogeog..."
...…the cytb gene were reported for salangid fishes, which are closely related to osmerids (Fu et al. 2005), and for galaxiid fishes of the southern hemisphere (Waters et al. 2000), which some authors consider to be closely related to Osmeroidei, too (Weitzman 1967; Fink and Weitzman 1982; Begle 1991)....
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11 citations
Cites background from "Molecular phylogenetics and biogeog..."
...But, during the early Tertiary, it too received an infusion of biota from South America via Antarctica and Australia....
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...A review of the origins of the New Zealand flora (Pole, 1994) indicates a close relationship to Australia, and that the present vegetation of the former is entirely, or almost entirely, the result of long distance dispersal during the Tertiary....
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...The ratite birds, moas and kiwis, probably arrived in the early Tertiary....
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...It seems that their evolution and distribution has occurred fairly recently, within the past 30 Ma, although there is a possibility that there may have been a transAntarctic dispersal in the earlier Tertiary (Waters et al., 2000)....
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...The majority of living genera and many families do not extend back beyond the Tertiary....
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TL;DR: The phylogenetic and biogeographical relationships of most representatives of the subtribe of Leptotina, using both likelihood and Bayesian approaches, are investigated, and phylogeographic patterns of the most widespread species, Leptotes pirithous are studied.
Abstract: Leptotina butterflies (Lycaenidae, Polyommatiinae) are found mostly in tropical and subtropical areas around the globe, marginally penetrating into temperate regions. Here, we investigated phylogenetic and biogeographical relationships of most representatives of the subtribe, using both likelihood and Bayesian approaches. We also estimated the timing of their diversification. And lastly, we studied phylogeographic patterns of the most widespread species, Leptotes pirithous. DNA sequences from two mitochondrial (COI, COII) and two nuclear genes (wingless, Ef1α) were analysed for 13 species of the genus Leptotes Scudder and one species of the genus Cyclyrius Butler. Both genera together form a monophyletic clade, and Cyclyrius is rooted deep inside Leptotes. Therefore, we designate Cyclyrius to be a junior synonym of Leptotes. According to our study, the genus Leptotes originated between the late Eocene and early Oligocene (35–31 Ma). During the Miocene it dispersed to the rest of the southern hemisphere, with further speciation events within the Indo‐Australian region, and separate radiations in the Americas and the Afrotropics. Leptotes webbianus from the Canary Islands turned out to be sister to the American clade from which it split c. 12 Ma. Leptotes pirithous originated in Madagascar c. 4 Ma and invaded the whole of Africa and southern Europe, including numerous surrounding islands. Populations of L. pirithous from Mauritius and Madagascar turned out to represent a distinct species (Leptotes durrelli sp.n.) and the same applies to the Australasian populations of Leptotes plinius (Leptotes lybas stat. rev.).
10 citations
Cites result from "Molecular phylogenetics and biogeog..."
...The results of other studies show that many classic Gondwanan groups combine an ancient vicariance pattern with relatively recent dispersal events (Waters et al., 2000; Cooper et al., 2001)....
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TL;DR: This spatio-temporal variability requires fishery regulations to be more tailored and flexible if they are to conserve the diversity of life-histories present in the catch and sustain the whitebait fishery.
Abstract: Whitebait comprise a culturally, commercially and recreationally important fishery in New Zealand, where post-larvae are netted while returning from their marine phase. In this study, we expanded a...
9 citations
Cites background from "Molecular phylogenetics and biogeog..."
...and Westland rivers (McDowall et al. 1998; Waters et al. 2000), but whitebait of the three...
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...%) of five whitebait species in samples (n≥ 100 fish) taken from eight rivers (plotted from north to south) over up to six months (July–December 2015). and Westland rivers (McDowall et al. 1998; Waters et al. 2000), but whitebait of the three endemic species must come from New Zealand....
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Dissertation•
31 Oct 2016
TL;DR: It is suggested that the manuscript should be rewritten in a chapters-by- chapters format to facilitate more detailed discussion of the author’s motivations and methods.
Abstract: ................................................................................................................................................ ii Acknowledgements ............................................................................................................................. iv Table of
8 citations
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...2009), freshwater fish (Waters et al. 2000), and cicadas (Arensburger et al....
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...Other New Zealand fauna, such as Lycosidae (wolf spiders; Vink & Paterson 2003), Zosterops (silvereye; Estoup & Clegg 2003), and galaxiid fish (Burridge et al. 2012; Waters et al. 2000), are...
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...While possible, this scenario is less likely than the dispersal scenario, which suggests Cantuaria landed in the newly-emerged New Zealand at a similar time to other biota (Perrie et al. 2003; Waters et al. 2000), and does not require Cantuaria’s substitution rate to be much slower than that of other mygalomorphs....
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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