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: Investigation of Galaxias vulgaris populations in New Zealand found that trout, rather than habitat, drove recruitment failure, and trout-free reaches appear to act as sources in a river network but are susceptible to future invasions by trout.
Abstract: Introduced predators with patchy distributions can create demographic sinks within native prey populations. Such invasions may give rise to source-sink metapopulations if there are still sources of native species colonists in the landscape. In New Zealand, introduced brown trout (Salmo trutta) and rainbow trout (Oncorhychus mykiss) are linked with declines in native non-diadromous galaxiids but co-occur with these galaxiids in some locations. We investigated whether trout create sinks in Galaxias vulgaris populations, and whether trout-free reaches could act as sources, allowing persistence in the sink habitat. We conducted quantitative seasonal monitoring of G. vulgaris population structure across two subcatchments of the Waimakariri River, South Island. Two trout-free and seven trout-invaded sites in the Porter River catchment and two trout-free and five trout-invaded sites in the Broken River catchment were monitored over two winters and the adjoining summer. Spatially continuous monitoring of young-of-the-year (YOY) galaxiid distributions and apparent survival across the Broken River catchment was also undertaken. Galaxias vulgaris YOY recruitment was high in trout-free reaches, indicating positive population growth. Galaxias vulgaris was absent from three trout-invaded sites, and the remaining invaded sites had significantly depleted juvenile recruitment. Information-theoretic model selection indicated that trout, rather than habitat, drove recruitment failure. Trout-invaded sites could be divided into "sinks" that retained no YOY galaxiids, indicating no local recruitment, and "pseudosinks," which had very few recruits. Absence of small G. vulgaris at sink sites suggested population maintenance through immigration of adults from sources, whereas pseudosink sites appear capable of self-recruitment at low carrying capacities. Trout-free reaches appear to act as sources in a river network but are susceptible to future invasions by trout. Thus, not only may invasive species cause source-sink metapopulations in native species, but also the potential of refugia for natives (sources) to become future sinks highlights the vulnerability of these metapopulations when invasive predators are the principal demographic driver.
50 citations
TL;DR: Galaxiid fishes are commonly assumed to exhibit a Gondwanan distribution, but little fossil evidence has been available to support or refute this assumption until now as mentioned in this paper, which is the only certain Galaxias fossils, and provide unequivocal evidence that the genus was abundant and taxonomically and ecologically diverse in the New Zealand region before 23 million years ago.
Abstract: Galaxiid fishes are commonly assumed to exhibit a Gondwanan distribution, but little fossil evidence has been available to support or refute this assumption until now. Here we report on three species of fossil Galaxias, represented by exquisitely preserved, almost entire skeletons, together with jaw and skull fragments, from several Miocene lacustrine deposits in Otago, South Island, New Zealand. These are the only certain Galaxias fossils, and provide unequivocal evidence that the genus was abundant, and taxonomically and ecologically diverse in the New Zealand region before 23 million years ago. One new species, Galaxias effusus, from an Early Miocene diatomite deposit near Middlemarch is described on the basis of low vertebral count, short caudal peduncle, expansive dorsal, caudal and anal fins, rounded to truncate caudal fin, with 15 principal caudal fin rays. The intact skeletons of G. effusus confirm that they inhabited a deep, stratified maar lake with cool, anoxic bottom water. The maar l...
46 citations
TL;DR: This paper used mtDNA and isozyme analysis of a freshwater fish, Galaxias divergens (Osmeriformes: Galaxiidae), to test a hypothesis of drainage evolution in South Island, New Zealand.
Abstract: We used mtDNA and isozyme analysis of a freshwater fish, Galaxias divergens (Osmeriformes: Galaxiidae), to test a hypothesis of drainage evolution in South Island, New Zealand. Geological evidence indicates that the presently north-flowing Kaituna River branch of the Pelorus River system once flowed south into the Wairau River system. The subsequent flow-reversal is thought to have resulted from Pleistocene subsidence in central New Zealand. mtDNA sequence data corroborated this geological hypothesis: rivers draining into Pelorus Sound were found to retain a genetic lineage of G. divergens that is otherwise restricted to the Wairau River system and adjacent coastal drainages (based on current sampling). Other sampled drainages in northern South Island and southern North Island were found to house lineages that were highly divergent from the Wairau‐Pelorus clade. Isozyme data yielded groupings based on fixed differences that were largely congruent with mtDNA clades. Standard molecular calibrations suggest that vicariant isolation of Pelorus and Wairau systems (drainage reversal) occurred in the mid-Pleistocene rather than the late Pleistocene as suggested by geology. Future multidisciplinary analyses will aim to improve our understanding of geological and molecular evolutionary rates. © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 88 , 367‐376.
45 citations
01 Jan 2010
TL;DR: In this article, the authors employ a variety of nuclear DNA loci to re- assess evolutionary relationships within a recent freshwater fish radiation to reappraise modes of speciation in New Zealand's freshwater-limited Galaxias vulgaris complex.
Abstract: Mechanisms of speciation are best understood in the context of phylogenetic relationships and as such have often been inferred from single gene trees, typically those derived from mitochondrial DNA (mtDNA) markers. Recent studies, however, have noted the potential for phylogenetic discordance between gene trees and underlying species trees (e.g., due to stochastic lineage sorting, introgression, or selection). Here, we employ a variety of nuclear DNA loci to re- assess evolutionary relationships within a recent freshwater fish radiation to reappraise modes of speciation. New Zealand's freshwater-limited Galaxias vulgaris complex is thought to have evolved from G. brevipinnis, a widespread migratory species that retains a plesiomorphic marine juvenile phase. A well-resolved tree, based on four mtDNA regions, previously sug- gested that marine migratory ability has been lost on 3 independent occasions in the evolution of this species flock (assum- ing that loss of diadromy is irreversible). Here, we use pseudogene (galaxiid Numt: 1801 bp), intron (S7: 903 bp), and exon (RAG-1: 1427 bp) markers, together with mtDNA, to reevaluate this hypothesis of parallel evolution. Interestingly, parti- tioned Bayesian analysis of concatenated nuclear sequences (3141 bp) and concatenated nuclear and mtDNA (4770 bp) both recover phylogenies implying a single loss of diadromy, not three parallel losses as previously inferred from mtDNA alone. This phylogenetic result is reinforced by a multilocus analysis performed using Bayesian estimation of species trees (BEST) software that estimates the posterior distribution of species trees under a coalescent model. We discuss factors that might explain the apparently misleading phylogenetic inferences generated by mtDNA. (Coalescence; Galaxiidae; incongruence; introgression; life history; mitochondrial DNA; nuclear copy; parallel evolution.)
45 citations
TL;DR: The authors' data support the separate species status of G. «southern» and G. gollumoides under both biological and phylogenetic species concepts, and suggest that the speciation of these taxa occurred in allopatry through independent losses of diadromy, with sympatry resulting from secondary contact.
Abstract: New Zealand's South Island houses a flock of closely related stream-resident fish taxa ( Galaxias vulgaris sensu lato ), including a number of species recently described on the basis of subtle morphological differences. The taxonomic status of some members of the species complex remains uncertain. This study examines the degree of reproductive isolation between recently recognized morphotypes from Southland ( G. «southern» , flatheads G. gollumoides , roundheads) which co-occur in Bushy Creek, a tributary of the Mataura R. Although these morphotypes are broadly sympatric in Southland and Stewart Island, Bushy Creek is their only documented zone of contact. Molecular (microsatellite, isozyme and mtDNA markers) and morphological analyses of 139 fish samples across a 500-m transect (seven stations) reveal a cline from predominantly G. «southern» ( N =85) to predominantly G. gollumoides ( N =54), corresponding with a gradual increase in stream gradient. Multivariate analyses of genotypic and morphological data independently reveal distinct clusters that are completely congruent with mtDNA type, suggesting an absence of mtDNA introgression. Our data support the separate species status of G. «southern» and G. gollumoides under both biological and phylogenetic species concepts. We suggest that the speciation of these taxa occurred in allopatry through independent losses of diadromy, with sympatry resulting from secondary contact.
44 citations
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