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: This work used mitochondrial DNA sequences (D-loop) to investigate the consequences of Quaternary glacial cycles over the pattern of genetic diversity and structure of G. maculatus along two biogeographical provinces in the Chilean coast.
Abstract: Major geologic and climatic changes during the Quaternary exerted a major role in shaping past and contemporary distribution of genetic diversity and structure of aquatic organisms in southern South America. In fact, the northern glacial limit along the Pacific coast, an area of major environmental changes in terms of topography, currents, and water salinity, represents a major biogeographic transition for marine and freshwater species. We used mitochondrial DNA sequences (D-loop) to investigate the consequences of Quaternary glacial cycles over the pattern of genetic diversity and structure of G. maculatus (Pisces: Galaxiidae) along two biogeographical provinces in the Chilean coast. Extreme levels of genetic diversity and strong phylogeographic structure characterize the species suggesting a low amount of influence of the last glacial cycle over its demography. However, we recognized contrasting patterns of genetic diversity and structure between main biogeographical areas here analyzed. Along the Intermediate Area (38°–41° S) each estuarine population constitutes a different unit. In contrast, Magellanic populations (43°–53° S) exhibited low levels of genetic differentiation. Contrasting patterns of genetic diversity and structure recorded in the species between the analyzed biogeographic areas are consistent with the marked differences in abiotic factors (i.e., different coastal configurations, Quaternary glacial histories, and oceanographic regimes) and to inherent characteristics of the species (i.e., salt-tolerance, physiology, and reproductive behavior).
27 citations
TL;DR: Divergence time estimates indicate that chance oceanic dispersal subsequent to Gondwanan fragmentation best explains the Southern Hemisphere radiation of cheilodactylids.
26 citations
TL;DR: Se llevo a cabo un analisis cladistico entre 70 taxones terminales de 20 ordenes diferentes y 271 caracteres morfologicos, principalmente en relacion with estructuras osteologicas y miologicas de la region cefalica, cintura escapular y las aletas anteriores y vertebras.
Abstract: A pesar de los avances realizados en relacion a la filogenia de los teleosteos en las ultimas decadas, los estudios recientes siguen planteando cuestiones relativas a los altos niveles de relacion de este notable grupo de diversos peces. El principal objetivo del presente trabajo es contribuir a aclarar los altos niveles de relacion de teleosteos. Con este proposito, se llevo a cabo un analisis cladistico entre 70 taxones terminales de 20 ordenes diferentes y 271 caracteres morfologicos, principalmente en relacion con estructuras osteologicas y miologicas de la region cefalica, cintura escapular y las aletas anteriores y vertebras. En el cladograma de consenso obtenido, los elopomorfos aparecen como los teleosteos mas basicos existentes. Los osteoglosomorfos incluidos en el analisis se agrupan en un ciado monofiletico, que es el grupo hermano de los restantes teleosteos no elopomorfos. Los Otocephala, los clupeiforines, y los ostariofisios aparecen como ciados monofileticos, contradiciendo asi los resultados de algunos analisis moleculares cladisticos recientes incluyendo los Alepocephalidae dentro Otocephala. De hecho, la monofilia de los Argentiniformes (Alepocephaloidea + Argentinoidea) esta bien apoyada por el analisis cladistico del presente trabajo. Este analisis cladistico tambien proporciona apoyo para la monofilia de los Alepocephaloidea, de los Argentinoidea, de los Galaxioidea + Osmeroidea, y de los Esociformes. Sin embargo, no proporciona pruebas solidas para resolver las relaciones entre los Argentiniformes, Salmoniformes, Esociformes, Osmeriformes y Neoteleostei, aunque indica que los salmoniformes podrian estar estrechamente relacionados con los Neoteleostei, y que los Esociformes y los Osmeriformes podrian constituir una unidad monofiletica. La monofilia de los Cypriniformes + Characiformes + Gymnotiformes + Siluriformes, de los Characiformes + Gymnotiformes + Siluriformes y de los Gymnotiformes + Siluriformes esta bien apoyada.
24 citations
Cites result from "Molecular phylogenetics and biogeog..."
...1), some studies have partially supported a closer relationship between esociforms and osmeriforms than between these latter fishes and the salmoniforms (see e.g. Waters et al., 2000: Figs....
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Journal Article•
TL;DR: Monophyly of the genus Gobiomorphus and all seven New Zealand species was strongly supported, and among the non-diadromous forms, species morphology contrasts with the molecular data suggesting a recent evolutionary history driven by ecological selection.
Abstract: Goal: To examine the phylogenetic relationships within Gobiomorphus to explore Australasian biogeography, origins (single or multiple), and evolutionary loss of a marine life stage (loss of diadromy). Methods: We analyse a fragment of the mitochondrial DNA (Cyt-b) using phylogenetic analyses, and use several meristics (spines, rays, and vertebrae) in a discriminant function analysis. Organisms: All nine species of the genus Gobiomorphus (Eleotridae) found in New Zealand and Australia, with the two Australian Philypnodon species included as outgroup taxa. Conclusions: Monophyly of the genus and all seven New Zealand species was strongly supported. The New Zealand Gobiomorphus are likely to be the result of a single introduction and to have been isolated from Australia since the Miocene or Pliocene (∼18–28 Myr ago). These dates correspond well to the oldest fossil in New Zealand dated at 16–20 Myr. Diadromy was consistently at the root of the New Zealand group, and non-diadromy and morphological diversification among these species appears to have occurred relatively recently, with meristic comparisons supporting the molecular analyses. However, among the non-diadromous forms, species morphology contrasts with the molecular data suggesting a recent evolutionary history driven by ecological selection.
24 citations
Cites background from "Molecular phylogenetics and biogeog..."
...…marine dispersal in Galaxias maculatus (Waters and Burridge, 1999; Waters et al., 2000a), as the sister relationship of Australian and New Zealand haplotypes conflicts with plate tectonics being responsible for their observed distributions (Waters et al., 2000b), as we found here for Gobiomorphus....
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...Molecular studies support the importance of marine dispersal in Galaxias maculatus (Waters and Burridge, 1999; Waters et al., 2000a), as the sister relationship of Australian and New Zealand haplotypes conflicts with plate tectonics being responsible for their observed distributions (Waters et al.,…...
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...…have revealed high rates of speciation in Galaxias divergens associated with non-diadromous life histories among different isolated catchments, while Allibone et al. (1996) and Waters et al. (2000a, 2000b) found that speciation within Galaxias species has been associated with the loss of diadromy....
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TL;DR: The molecular dates and phylogenetic estimates in this study are consistent with an Australasian origin for the Pomatiopsidae and an East to West radiation via Oligocene Borneo-Philippines island hopping to Japan and then China (Triculinae arising mid-Miocene in Southeast China), and less so with a triculine origin in Tibet.
Abstract: The Pomatiopsidae are reported from northern India into southern China and Southeast Asia, with two sub-families, the Pomatiopsinae (which include freshwater, amphibious, terrestrial and marine species) and the freshwater Triculinae. Both include species acting as intermediate host for species of the blood-fluke Schistosoma which cause a public health problem in East Asia. Also, with around 120 species, triculine biodiversity exceeds that of any other endemic freshwater molluscan fauna. Nevertheless, the origins of the Pomatiopsidae, the factors driving such a diverse radiation and aspects of their co-evolution with Schistosoma are not fully understood. Many taxonomic questions remain; there are problems identifying medically relevant species. The predicted range is mostly unsurveyed and the true biodiversity of the family is underestimated. Consequently, the aim of the study was to collect DNA-sequence data for as many pomatiopsid taxa as possible, as a first step in providing a resource for identification of epidemiologically significant species (by non-malacologists), for use in resolving taxonomic confusion and for testing phylogeographical hypotheses. The evolutionary radiation of the Triculinae was shown to have been rapid and mostly post late Miocene. Molecular dating indicated that the radiation of these snails was driven first by the uplift of the Himalaya and onset of a monsoon system, and then by late-Pliocene global warming. The status of Erhaia as Anmicolidae is supported. The genera Tricula and Neotricula are shown to be non-monophyletic and the tribe Jullieniini may be polyphyletic (based on convergent characters). Triculinae from northern Vietnam could be derived from Gammatricula of Fujian/Yunnan, China. The molecular dates and phylogenetic estimates in this study are consistent with an Australasian origin for the Pomatiopsidae and an East to West radiation via Oligocene Borneo-Philippines island hopping to Japan and then China (Triculinae arising mid-Miocene in Southeast China), and less so with a triculine origin in Tibet. The lack of monophyly in the medically important genera and indications of taxonomic inaccuracies, call for further work to identify epidemiologically significant taxa (e.g., Halewisia may be potential hosts for Schistosoma mekongi) and highlight the need for surveys to determine the true biodiversity of the Triculinae.
22 citations
Cites background from "Molecular phylogenetics and biogeog..."
...Numerous examples have been cited where the use of molecular clock rates for fishes led to estimated divergence dates either pre-dated the event attributed to their isolation [76-78] or the existence of their ancestral habitat [79,80]....
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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