*Department of Earth and Planetary Sciences, Nagoya University, Nagoya, Japan;
and
Ocean Research Institute, University of Tokyo, Tokyo, Japan
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Abstract |
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Introduction |
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We have recently shown that gamma-corrected distances based on amino acid sequences of two mitochondrial protein genes, i.e., NADH dehydrogenase subunit 2 (ND2) and cytochrome b (cytb) genes, provide a good estimate of pairwise distances between rather distantly related animals (Kumazawa, Yamaguchi, and Nishida 1999
; Kumazawa and Nishida 2000
). These distances were then used to calibrate molecular clocks of bony fishes under some reasonable assumptions and to suggest that the familial radiation of perciform fishes considerably predated the Cretaceous/Tertiary boundary, after which their fossil records concertedly appear (Kumazawa, Yamaguchi, and Nishida 1999
).
The present study focuses on fishes of the order Osteoglossiformes, one of the primary freshwater fish groups that are strictly intolerant of saltwater (Bn
rescu 1990
, pp. 4855, 6266). The osteoglossiforms are considered basal teleosts that preserve primitive anatomical features (e.g., the toothed tongue bones), but their individual members show peculiar specializations in morphology (e.g., elongate anal and dorsal fins), physiology (e.g., the air-breathing function of the swim bladder), and behavior (e.g., mouth brooding) (Nelson 1994
, pp. 9097; Greenwood and Wilson 1998
). These specializations or adaptations in morphology have contributed to obscure phylogenetic relationships of the osteoglossiforms (Bonde 1996
; Li and Wilson 1996
and references therein). In a standard classification by Nelson (1994
, pp. 9097), they were divided into two suborders, i.e., Osteoglossoidei and Notopteroidei (see table 1
). The former comprises arowanas (the family Osteoglossidae) and the butterflyfish (the only species in the Pantodontidae), whereas the latter includes mooneyes (Hiodontidae), Old World knifefishes (Notopteridae), elephantfishes (Mormyridae), and the aba (the only species in the Gymnarchidae). Extant osteoglossiforms are adapted to various (mostly tropical or subtropical) freshwater habitats in continents of Gondwanian origin with some exceptions, i.e., hiodontids in North America, two notopterid genera from South to Southeast Asia, and the Asian arowana in Southeast Asia (Nelson 1994
, pp. 9097).
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Molecular phylogenetic approaches may provide new insights into this question. To our knowledge, however, molecular phylogeny of the osteoglossiforms has not been fully investigated, except for mormyrid electric fishes (Alves-Gomes 1999
; Lavoué et al. 2000
). In this study, we thus analyzed the osteoglossoid phylogeny and divergence times using the two mitochondrial protein sequences expected to function as useful molecular markers for these issues.
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Materials and Methods |
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Amplification and sequence determination of the ND2 and cytb genes were carried out as previously described (Kumazawa, Yamaguchi, and Nishida 1999
). Primers designed to amplify and sequence the same genes of perciforms (Kumazawa, Yamaguchi, and Nishida 1999
) were useful in the present study. Amplified fragments purified with the QIAquick PCR purification kit (QIAGEN) were subjected to dye-terminator sequencing with the Applied Biosystems 373A DNA sequencer. Complete nucleotide sequences of the genes were unambiguously determined by reading both strands. The nucleotide sequence data reported in this study will appear in the DDBJ/EMBL/GenBank nucleotide sequence databases with the accession numbers AB035221AB035246.
Phylogenetic Analyses
Sequence alignment was conducted by eye with translated amino acid sequences of the osteoglossiforms as well as other taxa: the carp (Chang, Huang, and Lo 1994
), the loach (Tzeng et al. 1992
), the trout (Zardoya, Garrido-Pertierra, and Bautista 1995
), African and neotropical cichlids (Kumazawa, Yamaguchi, and Nishida 1999
), Amia calva (Kumazawa, Yamaguchi, and Nishida 1999
), the coelacanth (Zardoya and Meyer 1997
), sharks (Cao et al. 1998
; Delarbre et al. 1998
; Rasmussen and Arnason 1999a
), and a ray (Rasmussen and Arnason 1999b
). The alignment will appear in the EMBL database with the accession numbers ds43644 (ND2) and ds43645 (cytb). Amino acid sequences of the two genes were concatenated for phylogenetic analyses after gap sites were removed (723 alignable sites in total). Sharks and a ray were used as an outgroup.
Phylogenetic analyses using either nucleotide or amino acid sequences were conducted by three different methods: the maximum-parsimony (MP) method with PAUP, version 4.0b2 (Swofford 1999
), the neighbor-joining (NJ) method (Saitou and Nei 1987
) with njboot in Takezaki's Lintre package (Takezaki, Rzhetsky, and Nei 1995
), and the maximum-likelihood (ML) method with MOLPHY, version 2.3 (Adachi and Hasegawa 1996a
). Detailed conditions for each analytical method are described in table 2
. In this study, all pairwise distances used in the NJ analyses were corrected using a gamma parameter representing the extent of rate heterogeneity over sites. The importance of incorporating this parameter into deep-branch phylogenetic analyses has been widely recognized in previous literature that dealt with broad taxonomic groups (see, e.g., Kumazawa and Nishida 1999, 2000
; Mindell et al. 1999
; Takezaki and Gojobori 1999
).
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The clock of bony fishes was calibrated as in our previous study (Kumazawa, Yamaguchi, and Nishida 1999
), with minor modifications. First, we previously used eight sharks as chondrichthyan species, but here we used three sharks and a ray. This change had negligible effect on the calibration but saved computational time for the phylogenetic analyses. Second, we previously used PUZZLE, version 4.0 (Strimmer and von Haeseler 1996
), for estimating gamma-corrected ML distances (Kumazawa, Yamaguchi, and Nishida 1999
). However, these distances later turned out to be slightly overestimated due to errors in the mtREV24 matrix of PUZZLE 4.0, as noted in PUZZLE's online manual (http://www.tree-puzzle.de/manual.html). In this study, we thus used PAML 2.0 (Yang 1999
) for estimating gamma-corrected ML distances and confirmed that they were consistent with the values obtained using PUZZLE, version 4.0.2, in which the mtREV error was fixed.
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Results |
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Phylogenetic Relationship Within Osteoglossiformes
The molecular trees (fig. 1
and table 2
) support monophyly of the osteoglossiform species with high bootstrap values in relation to the other teleostean groups used in this study (see node i). Consistent with current ichthyological classification based on morphology (Nelson 1994
, pp. 15), the osteoglossiforms branched off basally from teleosts before the divergence of ostariophysans (carp and loach) from the lineage leading to protacanthopterygians (trout) and acanthopterygians (cichlids). Within the order Osteoglossiformes, monophyly of the osteoglossid species was supported with high bootstrap probabilities at node e. However, the relationship among the osteoglossids, notopterids, and mormyrids remained unresolved in our molecular analyses, because different tree-building methods supported different clustering patterns among them (table 2
).
The molecular trees consistently showed an unexpected phylogenetic affinity of the butterflyfish with the notopterids, although bootstrap support at node j varied considerably depending on the method used (table 2
). Morphological studies suggested that this species could be the sister group of either one (osteoglossines) or both (osteoglossines and heterotidines) osteoglossid subfamilies (Taverne 1979
; Lauder and Liem 1983
; Nelson 1994
, pp. 9097; Bonde 1996
; Li and Wilson 1996
). If this untraditional relationship really is the case, a number of synapomorphies defining the suborders Osteoglossoidei and Notopteroidei (see, e.g., Lauder and Liem 1983
; Li and Wilson 1996
) need to be reconsidered. Thus, although the phylogenetic affinity of the butterflyfish to the notopterids is currently the most straightforward interpretation of the molecular data, it will need to be further evaluated in the future. Within the family Osteoglossidae, two distinct lineages representing the osteoglossines and heterotidines were recognized, albeit with weaker bootstrap support for the osteoglossine monophyly. This is in agreement with previous morphological studies (Lauder and Liem 1983
; Bonde 1996
; Li and Wilson 1996
). The Osteoglossinae and the Heterotidinae have distinct morphological characteristics with regard to, e.g., the presence or absence of mandibular barbels and the number of branchiostegal rays (Nelson 1994
, pp. 9097).
As for the topological relationships among the five osteoglossine species, the molecular trees were in good agreement with the traditional classification (Nelson 1994
, pp. 9097). Two species of Osteoglossum make a sister clade to the Scleropages species, among which two morphologically more similar species in Australasia form a sister clade to the Asian species. Moderately high (nodes a and b) to very strong (node d) bootstrap support was obtained. In spite of these topological consistencies with the traditional classification, the molecular phylogeny had an unexpected feature. The divergences among three Scleropages species (nodes a and b) were much deeper than expected from the fact that they were classified within the same genus (see fig. 1
). This became conspicuous by comparison with the depth of divergences between mormyrid genera and among cichlid genera. The three Scleropages species may thus be more appropriately classified into different genera, at least from the molecular standpoint. In contrast, the divergence between two Osteoglossum species is reasonably shallow in light of their classificatory status. These observations, in turn, highlight the exceptionally high morphological conservation among the Scleropages species. Further support for this argument was obtained by quantitative evaluation of the depth of each divergence point (see below). Of course, we are aware that taxonomic ranks should not be determined from molecular divergence values only. Further study should be expected to scrutinize our proposition to revise the classificatory status of the genus Scleropages.
Rate Constancy Test, Clock Calibration, and Divergence Time Estimation
In order to use molecular sequence data as the molecular clock, the homogeneity of modes and rates of sequence evolution among lineages must be carefully examined. PUZZLE 4.0.2 (Strimmer and von Haeseler 1996
) uses a chi-square analysis to test at the 5% level whether the amino acid composition of each taxon is identical to the average composition among all taxa. We performed this test using the ND2/cytb amino acid sequences and confirmed that no taxon had a significantly deviated amino acid composition (data not shown).
Relative-rate tests (the two-cluster test; Takezaki, Rzhetsky, and Nei 1995
) were then conducted using the gamma-corrected amino-Poisson distances among the 28 taxa. Since sharks and a ray were used as an outgroup, evolutionary rates were compared between clusters created by all nonchondrichthyan nodes of the tree shown in figure 1
. The test showed, with a 99% significance level, that the lineage leading to the northern barramundi may have experienced a significantly accelerated molecular evolution compared with that leading to the spotted barramundi after their divergence at node b (data not shown). This rate inequality was not found between clusters at any other internal node. We thus excluded the northern barramundi from subsequent analyses. After that, the clock hypothesis held firm for all of the internal nodes.
When the significance level was lowered to 95%, external lineages leading to the Nile arowana and to the pirarucu were also found to possibly have different evolutionary rates. However, no other clusters created by any internal node, including those for cichlids, were found to have different rates (data not shown). We retained both of the heterotidines for subsequent analyses, allowing a somewhat unreliable estimation of the divergence time at node f. However, this did not affect the reliability of estimated times at the other internal nodes. Removal of either of the Nile arowana or the pirarucu had a negligible effect on them (data not shown). Taken together, these results indicate that there is no significant rate difference between the osteoglossiforms and other groups of fishes, which can justify the use of the clock calibrated using nonosteoglossiform fishes for estimating divergence times among the osteoglossiforms.
For the time estimation, we used gamma-corrected ML and Poisson distances of the ND2/cytb amino acid sequences that have been shown to correct multiple substitutions most effectively (see Materials and Methods). Figure 2 shows that the clock for bony fishes can be calibrated consistently using the reasonable assumption of continental vicariance of cichlids and two external calibration points based on reliable time estimates from independent molecular and/or paleontological evidence. A regression line through the origin (5.4 x 10-4 substitutions/site/Myr) was used as the clock to infer divergence times among the osteoglossiform taxa (table 3 ). Similar divergence times were obtained using two independent distance measurements, i.e., gamma-corrected ML and Poisson distances.
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Discussion |
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Although extant osteoglossiforms inhabit terrestrial regions mostly of Gondwanian origin, fossil evidence suggests their once worldwide distribution (Lundberg 1993
; Bonde 1996
; Li and Wilson 1996
). This is consistent with our molecular evidence suggesting that not only did the order Osteoglossiformes originate before Pangea began to be fragmented, but also its diversification into individual (sub)families (see values at nodes e, g, i, and j in table 3
). On the other hand, the estimated divergence time between two osteoglossine genera (172 ± 19 MYA at node c, table 3
) overlaps the period when Pangea separated into Laurasia and Gondwanaland (Smith, Smith, and Funnell 1994
; the Plates Project 1998
). It thus seems possible that the two genera originated and evolved primarily on Gondwanaland. The divergence time between black and silver arowanas at node d (26 ± 6 MYA) was small enough to deduce that they evolved within the isolated South American landmass.
Origin and Migrational Pathway of the Asian Arowana
As discussed above, the genus Scleropages possibly originated and evolved on Gondwanaland after the breakup of Pangea. However, one of its members, the Asian arowana, now inhabits a part of Eurasia. How can this be explained? Figure 3
illustrates three models for this zoogeographically interesting question, and we discuss the validity of each model in light of the molecular and geological evidence.
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Model B of figure 3
shows that the Asian arowana arose relatively recently via the transmarine dispersal of an Australasian arowana after plate tectonics moved Australia and New Guinea into the proximity of Southeast Asia (Bn
rescu 1995
, pp. 13491354, 1400). If this model were the case, the divergence time between the Asian and Australasian arowanas would be quite recent (<23 MYA). However, the molecular time estimate (138 ± 18 MYA) was much older (table 3
), making this model unlikely. Another argument against the dispersal of a Scleropages species in this model comes from the fact that Southeast Asia and Australasia belong to two distinct zoogeographical regions bordered by Wallace's Line (B
n
rescu 1995
, pp. 13491354) and that the freshwater ichthyofauna was considered to be one of the most conspicuous indices discriminating the two zoogeographical regions (Briggs 1987
, pp. 4555). Some authors (see, e.g., Lundberg 1993
; Briggs 1995
, pp. 290292) suggested the transmarine dispersal of euryhaline Scleropages populations by pointing out the existence of osteoglossid fossils found in saltwater beds (i.e., some of the Late Cretaceous to Eocene phareodontines, reviewed in Bonde [1996
]). However, this is not a straightforward idea. Extant Scleropages species are highly adapted to freshwater, and their fossils are found only in freshwater beds (Sanders 1934
).
Model C of figure 3
is a new model that is consistent with the molecular evidence. It assumes that ancestors of the Asian and Australasian arowanas diverged in the eastern margin of Gondwanaland during the Early Cretaceous (112146 MYA) and that the former was transported northward across the Tethys Sea (the paleo-Indian Ocean) on the Indian subcontinent. During the Jurassic, India-Madagascar and Australia were connected through Antarctica in the eastern margin of Gondwanaland (Smith, Smith, and Funnell 1994
; the Plates Project 1998
). India-Madagascar was separated from Gondwanaland 120130 MYA (Smith, Smith, and Funnell 1994
; the Plates Project 1998
) or somewhat more recently (Krause et al. 1997
), whereas Australia remained close to Antarctica during the Cretaceous and even the Early Tertiary. The estimated divergence time between the Asian and Australasian arowanas (138 ± 18 MYA) is close to or slightly larger than the probable time of the India-Madagascan separation from Gondwanaland, which is consistent with the idea that the Asian arowana originated on a part of Gondwanaland and was carried by the Indian subcontinent. Moreover, model C can naturally explain the peculiar localization of extant Scleropages species, and there is no need to invoke a saltwater adaptation of this primary freshwater fish group.
There are some fossil records of Scleropages which should be considered in evaluating the migrational history of the Asian arowana. Freshwater beds of Eocene times (3557 MYA) in central Sumatra yielded fossils that could be attributed to the genus Scleropages (Sanders 1934
). The Indian subcontinent became connected to Eurasia by the late Early Eocene (Jaeger, Courtillot, and Tapponnier 1989
; Metcalfe 1999
). Thus, the fossilized Scleropages in central Sumatra could have come from India through terrestrial freshwater habitats soon after their disembarkation from the Indian subcontinent.
Another intriguing possibility is that the Asian arowana was carried by smaller terranes (continental blocks) (e.g., the Sikuleh, Natal, and Bengkulu) that drifted from the Australian part of Gondwanaland in the Late Jurassic (146157 MYA) and were annexed to Southeast Asia in the Late Cretaceous (65112 MYA) (reviewed in Metcalfe 1999
). These three terranes actually accreted to Sumatra, the place where the fossilized Scleropages was found (Sanders 1934
). Given the Late Jurassic separation of these terranes, the estimated divergence time between the Scleropages species (138 ± 18 MYA) may appear somewhat late to support this explanation. However, because the history of Gondwanian landmasses in Southeast Asia has not fully been revealed (Metcalfe 1999
), we do not exclude the possibility that model C holds with one such terrane rather than with the Indian subcontinent.
Molecular Clocks of Bony Fishes
Molecular clocks of bony fishes have been studied using a variety of taxa, genes, and assumptions (see, e.g., Martin and Palumbi 1993
; Ortí et al. 1994
; Murphy and Collier 1996
; Bermingham, McCafferty, and Martin 1997
; Penzo et al. 1998
; Zardoya and Doadrio 1999
). Since most of these clocks are based on nucleotide sequences of relatively closely related taxa, little is known as to whether these clocks can be reliably extrapolated for divergences well over 100 MYA in time. For these old divergences, it seems reasonable to use amino acid sequences or nucleotide sequences without third codon positions, which are prone to be saturated quickly (Kocher et al. 1995
).
In this study, we thus used amino acid sequences of two mitochondrial protein genes. In spite of the general idea that quickly evolving mitochondrial sequences are not suited for dating deep divergences, gamma-corrected distances from the mitochondrial protein sequences were shown to correct multiple substitutions efficiently (Kumazawa and Nishida 2000
). The rate of the molecular clock for bony fishes using these distances was found to be nearly the same as or slightly faster than that for sharks but about three times as slow as that for mammals (Kumazawa, Yamaguchi, and Nishida 1999
). This profile for the rate difference between fishes and mammals is consistent with previous work using transversion substitutions at fourfold-degenerate sites (Martin, Naylor, and Palumbi 1992
) and restriction fragment length polymorphisms (Martin and Palumbi 1993
).
Long Lack of Fossil Records?
Our molecular evidence suggested a Paleozoic origin of the order Osteoglossiformes (table 3
), which is considerably older than the first osteoglossiform fossil record in the Late Jurassic (Benton 1993
, p. 624). Although the molecular data did not resolve the relationship among the osteoglossids, notopterids, and mormyrids, these groups are likely to have diverged during Permian-Triassic times (table 3
). Fossil records for the three families and some supposedly related extinct groups have been found from the Cretaceous or later (Benton 1993
, p. 624; Bonde 1996
). Thus, there appears to be a time gap between molecular and fossil evidence. We interpret this apparent discrepancy to be indicative of the paucity of osteoglossiform fossil records rather than the inferiority of our molecular time estimates.
In this respect, it should be emphasized that our estimates were based on a reasonably calibrated molecular clock using well-corrected distances (Kumazawa, Yamaguchi, and Nishida 1999
; Kumazawa and Nishida 2000
; fig. 2
) and that the rate constancy test was carefully carried out. Another argument is that the clock rate is consistent with the fossil evidence for the divergence point between sarcopterygians and actinopterygians (see the legend of fig. 2
). Finally, in order to reconcile the molecular and paleontological time estimates on the osteoglossiforms, the clock rate would have to be roughly twice that of figure 2 . However, this would elevate the fish rate to close to the mammalian one and cause clear inconsistency with previous work (Thomas and Beckenbach 1989
; Martin, Naylor, and Palumbi 1992
; Adachi, Cao, and Hasegawa 1993
; Martin and Palumbi 1993
).
Fossils of bony fishes are not necessarily considered well preserved in general. Of 425 teleostean families, 181 (43%) are completely lacking in their fossil record, and 58 (24%) of the remaining 244 families having recognizable fossil records occur with only otoliths (Benton 1993
, pp. 621622). We thus suspect that there is a long unrecorded history for the osteoglossiforms in the Mesozoic. A similar lack of fossil records has also been suggested for perciform families (Kumazawa, Yamaguchi, and Nishida 1999
), some teleostean orders (Kumazawa, Yamaguchi, and Nishida 1999
), and mammalian and avian orders (Janke et al. 1994
; Hedges et al. 1996
; Cooper and Penny 1997
; Janke, Xu, and Arnason 1997
; Kumar and Hedges 1998
; Waddell et al. 1999
). The history of vertebrates based on the paleontological evidence has not been substantially changed in its broadscale pattern since the 19th century (Benton 1998
). However, these lines of molecular studies may cast a doubt on the accuracy of the well-accepted vertebrate histories or, at least, they may call for the histories to be questioned and reexamined by multidisciplinary approaches, including molecular evolutionary ones.
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Conclusions |
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At present, the time estimates in table 3 are based on only two protein genes and a few calibration points and thus may be considered approximate estimations. However, due to the difficulties in the clock calibration for deep-branch osteichthyan groups as outlined earlier, even a rough framework of their divergence times has not been established by molecular approaches. We consider that our time estimates should be scrutinized in the future with more sequences or with other calibrations and revised if necessary. Nevertheless, our conclusion drawn herein about the origin and migrational pathway of the Asian arowana seems robust, because the three possible models of figure 3 propose quite different divergence times between the Asian and Australasian arowanas.
Since the Asian arowana is highly valued as a noble aquarium fish in Asian countries, it has been threatened with extinction in its native localities due to overfishing (or illegal fishing) and trading (Goh and Chua 1999
, pp. 924). Given the premium that this species points to the dynamic plate tectonics across the paleo-Indian Ocean, more attention than ever should be paid to its conservation.
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Acknowledgements |
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Footnotes |
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1 Keywords: Osteoglossiformes
teleost fish
mitochondrial DNA
historical biogeography
fossil-based divergence time
molecular clock
2 Address for correspondence and reprints: Yoshinori Kumazawa, Department of Earth and Planetary Sciences, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan. E-mail: h44858a{at}nucc.cc.nagoya-u.ac.jp
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