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: The results confirm the hybrid origin of the South American biota: there has been surprisingly little biotic exchange between the northern tropical and the southern temperate regions of South America, especially for animals.
Abstract: The Southern Hemisphere has traditionally been considered as having a fundamentally vicariant history. The common trans-Pacific disjunctions are usually explained by the sequential breakup of the supercontinent Gondwana during the last 165 million years, causing successive division of an ancestral biota. However, recent biogeographic studies, based on molecular estimates and more accurate paleogeographic reconstructions, indicate that dispersal may have been more important than traditionally assumed. We examined the relative roles played by vicariance and dispersal in shaping Southern Hemisphere biotas by analyzing a large data set of 54 animal and 19 plant phylogenies, including marsupials, ratites, and southern beeches (1,393 terminals). Parsimony-based tree fitting in conjunction with permutation tests was used to examine to what extent Southern Hemisphere biogeographic patterns fit the breakup sequence of Gondwana and to identify concordant dispersal patterns. Consistent with other studies, the animal data are congruent with the geological sequence of Gondwana breakup: (Africa(New Zealand(southern South America, Australia))). Trans-Antarctic dispersal (Australia southern South America) is also significantly more frequent than any other dispersal event in animals, which may be explained by the long period of geological contact between Australia and South America via Antarctica. In contrast, the dominant pattern in plants, (southern South America(Australia, New Zealand)), is better explained by dispersal, particularly the prevalence of trans-Tasman dispersal between New Zealand and Australia. Our results also confirm the hybrid origin of the South American biota: there has been surprisingly little biotic exchange between the northern tropical and the southern temperate regions of South America, especially for animals.
868 citations
Cites background from "Molecular phylogenetics and biogeog..."
...Molecular clock estimates of divergence times show that many classic Gondwanan groups combine an ancient vicariance pattern with relatively recent dispersal events (Waters et al., 2000b; Cooper et al., 2001), whereas other groups originated after continental breakup, and their distribution can be explained only by long-distance dispersal across oceanic barriers (Baum et al....
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...…estimates of divergence times show that many classic Gondwanan groups combine an ancient vicariance pattern with relatively recent dispersal events (Waters et al., 2000b; Cooper et al., 2001), whereas other groups originated after continental breakup, and their distribution can be explained only…...
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...Marine dispersal in currents associated with the West Wind Drift is also invoked to explain sister-group relationships between New Zealand–Australian marine organisms (Fell, 1962; Waters et al., 2000a)....
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...…Perciformes (64) ST Farias et al., 1999 ((MAD, IND)(AFR, NSA)) TGP (1.00) 48 (SG) Galaxiidae: Teleostei, Osteichthyes, Osmeriformes (28) ST Waters et al., 2000b (AFR, AUS, SSA, NZ, NC) 60 (RG), 20 (SG)e Chamaeleonidae + Agamidae: Reptilia, Squamata, Acrodonta (70) ST Macey et al., 2000…...
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...…relatively recent dispersal events (Waters et al., 2000b; Cooper et al., 2001), whereas other groups originated after continental breakup, and their distribution can be explained only by long-distance dispersal across oceanic barriers (Baum et al., 1998; Waters et al., 2000a; Buckley et al., 2002)....
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TL;DR: This study represents the most extensive taxonomic sampling effort to date to collect new molecular characters for phylogenetic analysis of acanthomorph fishes, with new and reliable clades emerging from this study of the acanthomorphic radiation.
350 citations
Cites background or methods from "Molecular phylogenetics and biogeog..."
...These correspond to loop regions in the 28s data set (D3 domain from 342 to 356 and D12 domain from 676 to 686), and in the 16S data set (G10 region of Waters et al. (2000) or stem 40 of Miya and Nishida (1998) from positions 683–713)....
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...…(base-paired regions) and loops (non-paired regions) following the secondary structure models published for sternoptychids (Miya and Nishida, 1998), Pygocentrus nattereri (Ort ı and Meyer, 1996), Fundulus heteroclitus (Parker and Kornifield, 1996), and Galaxias brevipinnis (Waters et al., 2000)....
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...For instance, Waters et al. (2000) showed that the helices G8–G14 (encompassing variable regions from l to n) in the 16s model of Alves-Gomes et al. (1995) and Ort ı (1997) were improperly paired or absent in more divergent taxa, resulting in a large loop....
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...For the 12S and 16S rDNA date sets, we localized stems (base-paired regions) and loops (non-paired regions) following the secondary structure models published for sternoptychids (Miya and Nishida, 1998), Pygocentrus nattereri (Ort ı and Meyer, 1996), Fundulus heteroclitus (Parker and Kornifield, 1996), and Galaxias brevipinnis (Waters et al., 2000)....
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TL;DR: The galaxioid fishes are the dominant, most speciose group of freshwater fishes (with >50 species) in the lands of the cool southern hemisphere, with representatives in western and eastern Australia, Tasmania, New Caledonia, Lord Howe Island, New Zealand, the Chatham, Auckland and Campbell Islands, Patagonian South America.
Abstract: The galaxioid fishes are the dominant, most speciose group of freshwater fishes (with >50 species) in the lands of the cool southern hemisphere, with representatives in western and eastern Australia, Tasmania, New Caledonia, Lord Howe Island, New Zealand, the Chatham, Auckland and Campbell Islands, Patagonian South America (Chile, Argentina), the Falkland Islands and South Africa. The group is most diverse in Australia and New Zealand. Lepidogalaxiidae is found only in Australia, Retropinnidae in Australia and New Zealand, and Galaxiidae across the entire range of the group. Many species are in serious conservation crisis for a diversity of reasons, including habitat deterioration and possibly fisheries exploitation, but there is enduring and pervasive information that shows that the group has been seriously impacted by the acclimatisation of salmonid fishes originating in the cool-temperate northern hemisphere, particularly brown and rainbow trout. With few exceptions, where these trout have been introduced there has been major decline in the galaxioids, especially Galaxiidae, as a result of a complexly interacting series of adverse impacts from these introduced fishes. In some places, centrarchids and cichlids may also have adverse impacts. In addition, there appear to have been adverse impacts from the translocation of galaxioids into communities where they do not naturally occur. In many instances it appears that displacement of the galaxioids has led to a situation where galaxioids and salmonids no longer co-occur, owing either to displacement or predation, leading to fish communities in which there is no explicit evidence for displacement. These effects are resulting in the galaxioid fishes being amongst the most seriously threatened fishes known.
301 citations
Cites background from "Molecular phylogenetics and biogeog..."
...…the scope of the galaxioid fishes, and particularly about whether the various genera that are discussed in this account form a monophyletic group, i.e. whether they share a closest common ancestry (Gosline 1960; McDowall 1969; Johnson and Patterson 1996; Williams 1996, 1997; Waters et al. 2000b)....
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TL;DR: New Caledonia must be considered as a very old Darwinian island, a concept that offers many more fascinating opportunities of study, as it is contradicted by geological evidence indicating long Palaeocene and Eocene submersions and by recent biogeographic and phylogenetic studies.
Abstract: New Caledonia has generally been considered a continental island, the biota of which largely dates back to Gondwanan times owing to its geological origin and the presence of phylogenetic relicts. This view is contradicted by geological evidence indicating long Palaeocene and Eocene submersions and by recent biogeographic and phylogenetic studies, with molecular or geophysical dating placing the biota no older than the Oligocene. Phylogenetic relicts do not provide conclusive information in this respect, as their presence cannot be explained by simple hypotheses but requires assumption of many ad hoc extinction events. The implication of this new scenario is that all the New Caledonian biota colonized the island since 37 Ma Local richness can be explained by local radiation and adaptation after colonization but also by many dispersal events, often repeated within the same groups of organisms. Local microendemism is another remarkable feature of the biota. It seems to be related to recent speciation mediated by climate, orography, soil type and perhaps unbalanced biotic interactions created by colonization disharmonies. New Caledonia must be considered as a very old Darwinian island, a concept that offers many more fascinating opportunities of study.
267 citations
Cites background from "Molecular phylogenetics and biogeog..."
...2005) and galaxiid fishes (Waters et al. 2000), sisters respectively to an Australian and a New Zealand group, are dated as younger than 12 and 9 Myr ago, respectively....
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...The freshwater galaxiids, supposedly unable to disperse over the sea, were often considered a relict taxon, even though the occurrence of marine larvae is pervasive in this group (Waters et al. 2000)....
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...…al. 2006) Sapotaceae (Bartish et al. 2005) Proteaceae (Barker et al. 2007) Paratya (Page et al. 2005) diving beetles (Balke et al. 2007a, b) galaxiid (Waters et al. 2000) Tasmantis Scincidae (Smith et al. 2007) sandalwoods (Harbaugh & Baldwin 2007) separation from Australia fine-grained black…...
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...The New Caledonian freshwater shrimp genus Paratya (Page et al. 2005) and galaxiid fishes (Waters et al. 2000), sisters respectively to an Australian and a New Zealand group, are dated as younger than 12 and 9 Myr ago, respectively....
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TL;DR: A series of coordinated studies in New Zealand streams that address the effect of an exotic fish on indi- vidual behavior, population, community, and ecosystem patterns are cobbled together.
Abstract: Knowledge of the population biology of invading species will often be necessary to develop effective management procedures and policies. But because invaders can have unexpected indirect effects in food webs, invasion ecologists need to integrate processes at the population level and other ecological levels. I de- scribe a series of coordinated studies in New Zealand streams that address the effect of an exotic fish on indi- vidual behavior, population, community, and ecosystem patterns. Such case studies are important as an aid to the formulation of policy about invasions that are especially likely to become problematic. At the individ- ual level, grazing invertebrates showed changes in behavior as a result of the introduction of brown trout ( Salmo trutta ), a predator that exerts a very different selection pressure than do native fish. At the population level, trout have replaced nonmigratory galaxiid fish in some streams but not others, and have affected the distributions of crayfish and other large invertebrates. At the community level, trout have suppressed grazing pressure from invertebrates and are thus responsible for enhancing algal biomass and changing algal species composition. Finally, at the ecosystem level, essentially all annual production of invertebrates is consumed by trout (but not by galaxiids), and algal primary productivity is six times higher in a trout stream. This leads, in turn, to an increased flux of nutrients from the water to the benthic community. The trout invasion has led to strong top-down control of community structure and ecosystem functioning via its effects on individual be- havior and population distribution and abundance. Particular physiological, behavioral, and demographic traits of invaders can lead to profound ecosystem consequences that managers need to take into account.
251 citations
Cites background from "Molecular phylogenetics and biogeog..."
...The vulnerability of these nonmigratory galaxiids to high discharge during the recruitment period may be a ghost of diadromy past: their ancestors migrated as pelagic larvae to estuaries and oceans (Waters et al. 2000; Waters & Wallis 2001)....
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References
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TL;DR: In this article, a non-parametric statistical framework for testing the fit of one hypothesized phylogeny versus an alternative phylogeny is presented for testing hypotheses about relative rates of evolution among the various lineages.
Abstract: Recombinant DNA technology provides evolutionary biologists with another tool for making phylogenetic inference through contrasts of restriction endounuclease cleavage site maps or DNA sequences between homologous DNA segments found in different groups. This paper is limited to the problem of making phylogenetic inference from restriction site maps. Several methods for making such inference have already been used or proposed (Avise et al., 1979a, 1979b;NeiandLi, 1979; Ferris et al., 1981), but all these methods depend upon the assumption that shared restriction sites reflect common evolutionary origins and are not the result of convergent evolution. Unfortunately, convergent evolution occurs with high probability for this type of data (Templeton, 1983). In addition, data from several different restriction enzymes are generally pooled in these analyses. Recently, Adams and Rothman (1982) have examined the distributions of cleavage sites and related sequences for 54 restriction endonucleases. They concluded 1) that cleavage sites and related sequences are distributed non-randomly in most DNA sequences, 2) that there is considerable heterogeneity between different restriction enzymes (even those with recognition sequences of the same length) with respect to the number and distribution of their respective cleavage sites and related sequences, and 3) that inference of phylogenetic relationship based on distances will be biased. In addition, Brown et al. (1982) sequenced 896 base pairs of the mitochondrial DNA from humans and apes and concluded that about 90% of the substitutions were transitions. The predominance of transitions over transversions increases the probability of convergence over that expected when all base substitutions are assumed to be equally likely (Templeton, 1983). Therefore, a need exists for an algorithm of phylogenetic inference that deals more directly with the problem of convergent evolution and statistical inhomogeneity between different restriction enzymes. In this paper, I propose such an algorithm. After discussing the problem of estimation of a phylogenetic tree, the task of statistical testing is then addressed. First, I present a non-parametric statistical framework for testing the fit of one hypothesized phylogeny versus an alternative phylogeny. Second, non-parametric statistical procedures are presented for testing hypotheses about relative rates of evolution among the various lineages.
1,556 citations
TL;DR: Reconsideration of the generation time hypothesis to include physiological effects such as metabolic rate improves the theoretical underpinnings of molecular evolution.
Abstract: There is increasing evidence for variation in rates of nucleotide substitution among divergent taxonomic groups. Here, we summarize published rate data and show a strong relationship between substitution rate and body size. For instance, rates of nuclear and mtDNA evolution are slow in whales, intermediate in primates, and fast in rodents. A similar relationship exists for poikilothermic vertebrates. However, these taxa have slower mtDNA substitution rates overall than do homeotherms of similar size. A number of physiological and life history variables are highly correlated with body size. Of these, generation time and metabolic rate explain some patterns of rate heterogeneity equally well. In many cases, however, differences in metabolic rate explain important exceptions to the generation time model. Correlation between metabolic rate and nucleotide substitution may be mediated by (i) the mutagenic effects of oxygen radicals that are abundant by-products of aerobic respiration, and (ii) increased rates of DNA synthesis and nucleotide replacement in organisms with higher metabolic rates. Both of these factors increase mutation rate by decreasing the "nucleotide generation time," the average length of time before a nucleotide is copied either through replication or repair. Reconsideration of the generation time hypothesis to include physiological effects such as metabolic rate improves the theoretical underpinnings of molecular evolution.
1,151 citations
TL;DR: It is concluded that the use of the REV model in phylogenetic analysis can be recommended, especially for large data sets or for sequences with extreme substitution patterns, while HKY85 may be expected to provide a good approximation.
Abstract: Knowledge of the pattern of nucleotide substitution is important both to our understanding of molecular sequence evolution and to reliable estimation of phylogenetic relationships. The method of parsimony analysis, which has been used to estimate substitution patterns in real sequences, has serious drawbacks and leads to results difficult to interpret. In this paper a model-based maximum likelihood approach is proposed for estimating substitution patterns in real sequences. Nucleotide substitution is assumed to follow a homogeneous Markov process, and the general reversible process model (REV) and the unrestricted model without the reversibility assumption are used. These models are also applied to examine the adequacy of the model of Hasegawa et al. (J. Mol. Evol. 1985;22:160–174) (HKY85). Two data sets are analyzed. For the Ψν-globin pseudogenes of six primate species, the REV model fits the data much better than HKY85, while, for a segment of mtDNA sequences from nine primates, REV cannot provide a significantly better fit than HKY85 when rate variation over sites is taken into account in the models. It is concluded that the use of the REV model in phylogenetic analysis can be recommended, especially for large data sets or for sequences with extreme substitution patterns, while HKY85 may be expected to provide a good approximation. The use of the unrestricted model does not appear to be worthwhile.
1,051 citations
TL;DR: To estimate approximate divergence times of species or species groups with molecular data, a method of constructing a linearized tree under the assumption of a molecular clock is developed and used to analyze hominoid mitochondrial DNA and drosophilid Adh gene sequences.
Abstract: To estimate approximate divergence times of species or species groups with molecular data, we have developed a method of constructing a linearized tree under the assumption of a molecular clock. We present two tests of the molecular clock for a given topology: two-cluster test and branch-length test. The two-cluster test examines the hypothesis of the molecular clock for the two lineages created by an interior node of the tree, whereas the branch-length test examines the deviation of the branch length between the tree root and a tip from the average length. Sequences evolving excessively fast or slow at a high significance level may be eliminated. A linearized tree will then be constructed for a given topology for the remaining sequences under the assumption of rate constancy. We have used these methods to analyze hominoid mitochondrial DNA and drosophilid Adh gene sequences.
815 citations
TL;DR: Congruence of biological and geological area-cladograms at a high confidence level means that specified events of paleogeography can be adopted as an explanation of the biological patterns, and distributions of sedentary organisms have the potential to falsify dispersal theories as applied tovagile organisms, but distributions of vagile organisms cannot falsify vicariance theories as applications to sedentary ones.
Abstract: Rosen, D. E. (Department of Ichthyology, American Museum of Natural History, New York, New York 10024) 1978. Vicariant patterns and historical explanation in biogeography. Syst. Zool. 27:159-188.-Geographic coincidence of animal and plant distributions to form recognizable patterns suggests that the separate components of the patterns are historically connected with each other and with geographic history. To seek evidence of these historical connections, cladograms of geographic areas, representing sequences of disruptive geologic, climatic, or geographic events, may be compared with biological cladograms, representing sequences of allopatric speciation events in relation to those geographic areas. Such comparisons, when they meet the minimum requirements of being among dichotomized threetaxon cladograms, can resolve similar or dissimilar historical factors; two-taxon statements do not distinguish between groups with different histories. Congruence of biological and geological area-cladograms at a high confidence level (such as congruence of a five-taxon cladogram or four three-taxon cladograms with a geological cladogram, where the confidence level can be shown in cladistic theory to be 99%o) means that specified events of paleogeography can be adopted as an explanation of the biological patterns. In such a cause and effect relationship, where the earth and its life are assumed to have evolved together, paleogeography is taken by logical necessity to be the independent variable and biological history, the dependent variable. Drawing a mathematical simile, the biological cladogram y (dependent variable), is a function of the geological cladogram x (independent variable), as in a simple regression of effect y on cause x where we are given no free choice as to which is the independent variable. Such a view implies that any specified sequence in earth history must coincide with some discoverable biological patterns; it does not imply a necessary converse that each biological pattern must coincide with some discoverable paleogeographic pattern, because some biological distributions might have resulted from stochastic processes (chance dispersal). Determining that all discoverable biological patterns conflict with a given corroborated or observed sequence of geologic, climatic, or geographic change (i.e., that y is not a function of x), in theory, therefore should falsify vicariance biogeography. Because dispersal biogeography presupposes stochastic processes, and any failure to meet the expectation of a postulated dispersal is explained by an additional dispersal, dispersal biogeography is immune to falsification. Without resort to paleontology or earth history, whether a given historical relationship implied by congruence of biological area-cladograms is the result of dispersal or vicariance can also be thought of in terms which minimize the number of necessary assumptions: did the sedentary organisms disperse with the vagile ones or did the vagile organisms vicariate with the sedentary ones? Cladistic congruence of a group of sedentary organisms with a group of vagile ones rejects dispersal for both. Hence, distributions of sedentary organisms have the potential to falsify dispersal theories as applied to vagile organisms, but distributions of vagile organisms cannot falsify vicariance theories as applied to sedentary ones. The problems that arise in various kinds of historical explanation are exemplified by several specific distributions of fishes and other organisms in North and Middle America and in the larger context of Pangaean history, and are discussed in relation to current species concepts. [Vicariance; species concepts; biocladistics; biohistory; geocladistics; geohistory; Neotropics; Gondwanaland.]
786 citations
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...alternatives sometimes portrayed (Croizat et al., 1974; Rosen, 1978; Craw, 1979)....
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