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: Nine species are narrow-range endemics, known from one, or only a few, locations, and these restricted distributions most probably reflect the fragmentation and reduction of former ranges caused by the effects of alien salmonids.
Abstract: The systematics of the Galaxias olidus hyper-species complex from freshwater habitats in south-eastern, mainland Australia is revised. Galaxias olidus Gunther 1866 is redescribed, Galaxias fuscus Mack 1936 and Galaxias ornatus Castelnau 1873, previously synonymised with G. olidus (sensu lato), are reinstated as valid taxa and redescribed, and 12 taxa are described as new: Galaxias aequipinnis sp. nov., Galaxias arcanus sp. nov., Galaxias brevissimus sp. nov., Galaxias gunaikurnai sp. nov., Galaxias lanceolatus sp. nov., Galaxias longifundus sp. nov., Galaxias mcdowalli sp. nov., Galaxias mungadhan sp. nov., Galaxias oliros sp. nov., Galaxias supremus sp. nov., Galaxias tantangara sp. nov., and Galaxias terenasus sp. nov. These species are morphologically similar and, whilst there is extensive overlap in meristic counts and morphometric characters, each can be diagnosed by unique combinations of characters, including allozyme loci and colour pattern; morphological diagnosis is improved greatly if based on freshly formalin-fixed material. Galaxias schomburgkii Peters 1868, Galaxias bongbong Macleay 1881, Galaxias kayi Ramsay & Ogilby 1886 and Galaxias oconnori Ogilby 1912 are retained as junior synonyms of G. olidus (sensu stricto). The types for Galaxias findlayi Macleay 1882 are lost and no specimens matching its description were collected or examined from the Mt. Kosciuszko region; it is also currently retained as a junior synonym of Galaxias olidus s.s. The species G. terenasus sp. nov. and G. arcanus sp. nov. are the most morphologically specialised in the complex and G. olidus s.s remains the most morphologically variable species. It also remains the most widespread taxon, though its previously known distribution is reduced, particularly in the south-west of its range. Nine species are narrow-range endemics, known from one, or only a few, locations, and these restricted distributions most probably reflect the fragmentation and reduction of former ranges caused by the effects of alien salmonids. Eleven species are of conservation concern, most are considered critically endangered.
44 citations
TL;DR: All populations experienced Late Pleistocene-Holocene population growth, possibly in response to the relaxation of arid conditions after the last glacial maximum, and high levels of genetic divergence and the discovery of new cryptic species have important implications for the conservation of this already threatened group of freshwater species.
Abstract: The freshwater fauna of Southern Australia is primarily restricted to the southwestern and southeastern corners of the continent, and is separated by a large, arid region that is inhospitable to this biota. This geographic phenomenon has attracted considerable interest from biogeographers looking to explain evolutionary diversification in this region. Here, we employed phylogenetic and phylogeographic approaches to evaluate the effect of this barrier on a group of four galaxiid fish species (Galaxiella) endemic to temperate Southern Australia. We also tested if continental shelf width has influenced connectivity among populations during low sea levels when rivers, now isolated, could have been connected. We addressed these questions by sampling each species across its range using multiple molecular markers (mitochondrial cytochrome b sequences, nuclear S7 intron sequences, and 49 allozyme loci). These data also allowed us to assess species boundaries, to refine phylogenetic affinities, and to estimate species ages. Interestingly, we found compelling evidence for cryptic species in G. pusilla, manifesting as allopatric eastern and western taxa. Our combined phylogeny and dating analysis point to an origin for the genus dating to the early Cenozoic, with three of the four species originating during the Oligocene-Miocene. Each Galaxiella species showed high levels of genetic divergences between all but the most proximate populations. Despite extensive drainage connections during recent low sea levels in southeastern Australia, populations of both species within G. pusilla maintained high levels of genetic structure. All populations experienced Late Pleistocene-Holocene population growth, possibly in response to the relaxation of arid conditions after the last glacial maximum. High levels of genetic divergence and the discovery of new cryptic species have important implications for the conservation of this already threatened group of freshwater species.
44 citations
Cites background from "Molecular phylogenetics and biogeog..."
...[30] found Galaxiella species to be reciprocally monophyletic and most closely related to Brachygalaxias based on mitochondrial DNA sequences....
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TL;DR: This study appears to be the first example of an animal group displaying clear multiple east-west movement in southern Australia, as all other aquatic and terrestrial fauna previously examined displayed a single east- west split.
Abstract: The biogeography of southern Australia is characterized by a repeated pattern of relatedness between the biota of southwestern and southeastern Australia. Both areas possess a temperate climate but are separated by a vast arid region, currently lacking permanent freshwater habitats, which has become increasingly drier since about 15 Ma. Aquatic organisms have thus potentially remained isolated for a considerable time. Pygmy perches (Nannatherina and Nannoperca, Percichthyidae) provide an excellent scenario for investigating biogeographic relationships between southwestern and southeastern regions as multiple species occur on either side of Australia. This allows us to potentially differentiate between "Multiple Invasion" and "Endemic Speciation," the two major hypotheses proposed to account for current distributions. The first suggests that multiple east-west movements have occurred, whereas the second suggests a single east-west split, with current biodiversity in each region being reciprocally monophyletic. Systematic relationships within this group were investigated with the mitochondrial cytochrome b gene; nuclear intron and exon sequences from S7, RAG1, and RAG2; and 53 allozyme loci. Our data supported the hypothesis of multiple movements across southern Australia based on a consistent lack of support for reciprocal monophyly of eastern and western species. This study appears to be the first example of an animal group displaying clear multiple east-west movement in southern Australia, as all other aquatic and terrestrial fauna previously examined displayed a single east-west split. Despite a high degree of sympatry within each region, the only evidence for hybridization was found between Nannoperca australis and N. obscura, with the latter having its mitochondrial genome completely replaced by that of N. australis, with no evidence for nuclear introgression. This is one of only a few confirmed examples of complete replacement of the mitochondrial genome in one species with that of another. Cryptic differentiation was also evident within the two most widespread species, N. australis and N. vittata, indicating that these likely consist of multiple species. We also highlight the need for multiple molecular markers with different strengths in order to obtain a more robust phylogeny, despite problems resulting from potential incongruences between data sets.
42 citations
Cites background from "Molecular phylogenetics and biogeog..."
...Waters et al. (2000) did not specifically date the split between the two western and one eastern species, but when degree of separation between them was compared with dated nodes, it suggested the separation between the reciprocally monophyletic eastern and western Galaxiella species was not recent…...
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TL;DR: The endemic freshwater herring of the lake are the descendents of an ancient marine incursion, a scenario which may also explain the origin of other Tanganyikan endemics.
Abstract: The spectacular marine-like diversity of the endemic fauna of Lake Tanganyika, the oldest of the African Great Lakes, led early researchers to suggest that the lake must have once been connected to the ocean. Recent geophysical reconstructions clearly indicate that Lake Tanganyika formed by rifting in the African subcontinent and was never directly linked to the sea. Although the Lake has a high proportion of specialized endemics, the absence of close relatives outside Tanganyika has complicated phylogeographic reconstructions of the timing of lake colonization and intralacustrine diversification. The freshwater herring of Lake Tanganyika are members of a large group of pellonuline herring found in western and southern Africa, offering one of the best opportunities to trace the evolutionary history of members of Tanganyika's biota. Molecular phylogenetic reconstructions indicate that herring colonized West Africa 25–50MYA, at the end of a major marine incursion in the region. Pellonuline herring subsequently experienced an evolutionary radiation in West Africa, spreading across the continent and reaching East Africa's Lake Tanganyika during its early formation. While Lake Tanganyika has never been directly connected with the sea, the endemic freshwater herring of the lake are the descendents of an ancient marine incursion, a scenario which may also explain the origin of other Tanganyikan endemics.
40 citations
Cites background from "Molecular phylogenetics and biogeog..."
...Optimization of rDNA gene fragment alignments was facilitated through the use of secondary structure models for teleost long and short subunit RNAs [54,55]....
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TL;DR: A generally well-resolved phylogeny of the genera that conflicts with previous hypotheses of osmerid interrelationships is reconstructed, and Shimodaira-Hasegawa tests suggest the topology with the current molecular dataset is significantly better than earlier reconstructions.
39 citations
Cites background from "Molecular phylogenetics and biogeog..."
...This will not come as a surprise to anyone who has studied osmeroid fishes, as repeated losses and gains of particular character states have been noted by many authors (Johnson and Patterson, 1996, and references therein; Waters et al., 2000, 2002)....
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...16S 16Sar CGC CTG TTT ATC AAA AAC AT Waters et al. (2002)...
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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