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Volume 16, 2002 © CSIRO 2002

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Invertebrate Systematics, 2002, 16, 697–701

IT01 31 1N6.SPrMRNurAphvyarinadtoCn.iM.Austrainl n Macrobrachium

A preliminary study of 16S rRNA sequence variation in Australian Macrobrachium shrimps (Palaemonidae:Decapoda) reveals inconsistencies in their current classification Nicholas P. MurphyA and Christopher M. Austin School of Ecology and Environment, Deakin University, P.O Box 423, Warrnambool, Victoria 3280, Australia. A To whom correspondence should be addressed. Email: [email protected]

Abstract. The systematic relationships among Australian palaemonid shrimps have been the subject of speculation for some time. A preliminary phylogenetic study was undertaken to clarify the relationships of five species, Macrobrachium intermedium (Stimpson), M. australiense (Holthuis), M. atactum (Riek), M. rosenbergii (de Man) and Palaemon serenus (Heller), using 16S rRNA mitochondrial gene sequences. Phylogenetic analyses indicated inconsistencies with the current classification in two respects. First, M. intermedium formed a very well-supported clade with P. serenus distinct from M. australiense, M. atactum and M. rosenbergii. Second, the two species from inland Australia, M. australiense and M. atactum, showed a high level of genetic similarity over a substantial geographic range, suggesting that they may represent conspecific populations. The taxonomic and biogeographic implications of these findings for Macrobrachium in Australia are discussed.

Introduction Shrimps of the family Palaemonidae are a very successful group of decapod crustaceans that inhabit marine, estuarine and freshwater environments throughout the world. The palaemonids have historically been a taxonomically difficult group because they appear to be morphologically highly conservative (Holthuis 1950, 1952; Boulton and Knott 1984; Chow and Fujio 1985; Fincham 1987). Until recently, all major systematic treatments have been based on morphological characteristics alone (Holthuis 1950; Riek 1951; Fincham 1987). A few allozyme-based studies have been undertaken (e.g. Boulton and Knott 1984; Chow and Fujio 1985), but no systematic studies utilising DNA-based data have been published. This is surprising given that several species, including the giant freshwater prawn Macrobrachium rosenbergii (de Man), found throughout the Indo-Pacific region (including Australia) are important commercially, particularly in developing countries. In contrast, other important decapod crustacean groups, such as penaeid prawns, freshwater crayfish and marine lobsters, have been much more extensively studied using molecular genetic techniques (e.g. Palumbi and Benzie 1991; Bouchon et al. 1994; Crandall et al. 1999; Gusmão et al. 2000). In Australia, palaemonids are widespread, with representatives inhabiting marine, estuarine and freshwater environments. Boulton and Knott (1984), in a study of © CSIRO 2002

palaemonid species in the Swan River Estuary, Western Australia, using allozyme data, found inconsistencies between the current morphologically based classification system and genetic relationships between the species studied. They recommended the extension of their genetic studies to other Australian palaemonid species. As a consequence, a study has been initiated to investigate phylogenetic relationships among Australian palaemonid shrimp species using mtDNA sequences and to use these relationships to test the validity of the current morphologically based classification. Sequences from the 16S rRNA mitochondrial gene region have been found to be extremely useful for studying taxonomic questions and phylogenetic relationships within a number of crustacean groups (e.g. Bucklin et al. 1995; Crandall and Fitzpatrick 1996; Kitaura et al. 1998; Crandall et al. 1999). The 16S rRNA gene has both fast and slow evolving regions and therefore can provide useful information across a broad taxonomic spectrum from the population to the family level. The aim of this paper is to report the preliminary findings of a study of phylogenetic and taxonomic relationships among several Australian species of palaemonid shrimp determined from 16S rRNA mitochondrial gene region sequences. This study indicates inconsistencies with the current taxonomy of these shrimp at both the species and genus levels. 10.1071/IT01031

1445-5226/02/050697

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Materials and methods Taxa Four species of Australian Palaemonidae were looked at in this study, including three of the thirteen Australian members of the genus Macrobrachium: M. australiense (Holthuis) and M. atactum (Riek) found in inland waters of the eastern half of the continent and M. intermedium (Stimpson) found in estuarine and some marine waters around the southern coastline of Australia from Perth, WA to the central Queensland coast. The other palaemonid species included in this study is Palaemon serenus (Heller), a marine species with a similar distribution to M. intermedium. The giant freshwater prawn, Macrobrachium rosenbergii, was used for species-level comparative purposes, as it is a widespread and extensively studied Macrobrachium species. The widespread Australian atyid shrimp Paratya australiensis (Kemp) was chosen as the outgroup because the Atyidae belong to the Caridea (as do the Palaemonidae). The main morphological feature used to separate the two genera, Palaemon and Macrobrachium, is the presence of either the branchiostegal spine or the hepatic spine on the carapace. Macrobrachium species are distinguished by the absence of the former and presence of the latter, whereas Palaemon species are distinguished by the opposite arrangement (Holthuis 1950). The two inland species, M. australiense and M. atactum, are considered to be closely related and are separated on the basis of the presence/absence of long dense hairs on the second pereopod (Riek 1951). Sample collection Macrobrachium intermedium was collected from seagrass beds in the estuarine sections of the Hopkins River and Fitzroy River in south-western Victoria; Palaemon serenus was obtained from rock pools off Griffith Island, Port Fairy, Victoria; Macrobrachium atactum was obtained from the Thompson River, near Muttaburra, Queensland; Macrobrachium australiense was collected from the Murray River, New South Wales; Macrobrachium rosenbergii was collected from a small river near Madang, Papua New Guinea; and Paratya australiense was collected from the Hopkins River, Victoria. All specimens were collected using a dipnet and either frozen in liquid nitrogen immediately, stored in 95% ethyl alcohol, or transported live back to the laboratory and stored at –80°C. Voucher specimens were stored in 70% ethanol and have been housed in the Decapod Collection of Deakin University, School of Ecology and Environment. DNA extraction and amplification DNA was extracted from abdominal muscle tissue using a high salt precipitation method (Crandall et al. 1999). Segments of the 16S rRNA mitochondrial gene for each individual were amplified by polymerase chain reaction (PCR) using the L2510 (CGCCTCTTTAACAAGACAT) and H3062 (CCGGTCTGAACTCAGATCA) primers developed by Kitaura et al. (1998). Tissue from two individuals of each species was amplified in order to eliminate potential PCR errors (e.g. contamination, nuclear copies of mitochondrial DNA), mislabelling and misidentification of specimens during collection. Double-stranded PCR products were obtained in a total reaction volume of 50 µL, containing 5 µL of 10× PCR buffer (Invitrogen; www.invitrogen.com), 0.4 mM of each dNTP, 0.8 µM of each primer, 4 mM MgCl2, 1 unit of Taq polymerase (Invitrogen) and 2 µL of DNA extract. PCR amplification was carried out in a PC-960 microplate thermal sequencer (Corbett Research; www.corbettresearch.com) using the following temperature regime: an initial denaturation step of 95°C for 3 min, followed by 30 cycles of 95°C for 30 s, an annealing temperature of 50°C for 30 s and an extension temperature of 72°C for 30 s. This was then followed by an additional extension of 72°C for 3 min. PCR products were purified using a Qiagen (www.qiagen.com) QIAquick PCR purification kit,

N. P. Murphy and C. M. Austin

with final elution volumes of 50 µL per individual. The DNA concentrations were approximated against a Promega (www.promega.com) DNA/Hae111 marker on a 2% agarose/TAE gel containing ethidium bromide and viewed under UV light. Samples were sent to the Australian Genome Research Facility (AGRF), University of Queensland, for sequencing. Sequencing reactions followed the protocol of Perkin Elmer, using an ABI big dye terminator reaction with custom primers (www.appliedbiosystems. com). For each sample, sequencing was performed in both directions. Phylogenetic reconstruction Sequence chromatograms were viewed and edited manually using SeqPup software (http://iubio.bio.indiana.edu/soft/molbio/seqpup/ java). Once edited, multiple alignments were performed using Clustal X (Thompson et al. 1997) with multiple alignment parameters of gap penalty equal to 10–15, gap extension penalty equal to 3–5 and pairwise parameters of gap penalty equal to 3–5 and k-tuple of 1–3. Sequences were then imported into PAUP* 4.0b4a (Swofford 2000) for phylogenetic analysis. A chi-square analysis of homogeneity of base frequencies among taxa was carried out to determine whether any non-stationarity of base frequencies was evident. Pairwise sequence distances were calculated using the Hasegawa, Kishino and Yano (HKY) model (Hasegawa et al. 1985) of nucleotide sequence evolution and a neighbour joining tree was generated. The appropriate model of evolution for maximum likelihood (ML) analysis was obtained via testing alternative modes of evolution using Modeltest (Posada and Crandall 1998). The HKY + G (gamma; Yang 1993) model was chosen, with a ti/tv ratio of 1.5118 and a gamma distribution shape parameter of 0.368 for estimation of an ML tree. Trees were also estimated using a maximum parsimony (MP) analysis, via a branch and bound search, using random sequence addition with indels treated as a fifth base. Confidence in the trees generated by these methods was obtained using 1000 bootstrap pseudoreplications.

Results The sequence alignment yielded a total of 488 sites for phylogenetic analysis, of which 195 were variable. There were no discernable differences between sequences obtained from individuals of the same species. The mean total nucleotide composition was A = 31%, T = 35%, C = 12% and G = 22%, indicating that the 16S rRNA region of the mtDNA is adenine and thymine rich in the palaemonids. The chi-square analysis of separate base frequencies showed no significant deviation of stationarity among all taxa. Resulting sequences have been submitted to GenBank (AF374465–AF374469). There was 2% sequence divergence, based on the HKY distance matrix, between the two inland Macrobrachium species (M. atactum and M. australiense), whereas the mean sequence divergence between the inland Macrobrachium and the estuarine M. intermedium was 24%. In stark contrast, there was only 9% sequence divergence between M. intermedium and Palaemon serenus and 10% between the inland Macrobrachium species and M. rosenbergii. The distance between the outgroup, Paratya australiensis, and all palaemonid species (33–38%), is greater than for all pairwise comparisons between palaemonid species (Table 1).

16S rRNA variation in Australian Macrobrachium

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Table 1. The HKY pairwise distances (below diagonal) and number of nucleotide substitutions (above diagonal) between four Australian Palaemonidae, a related widespread species (Macrobrachium rosenbergii) and outgroup, Paratya australiensis, for 488 base pairs of 16S rRNA mitochondrial sequences 1 1. Palaemon serenus 2. Macrobrachium intermedium 3. M. australiense 4. M. atactum 5. M. rosenbergii 6. Paratya australiensis

0.094 0.257 0.258 0.267 0.381

2

3

4

5

6

41

100 096

100 096 7

93 88 40 40

137 130 128 128 120

0.245 0.244 0.249 0.359

0.015 0.103 0.353

0.103 0.352

0.338

suggesting that it showed a number of atypical morphological features for the genus and he grouped it, using cladistic and cluster analyses, nearer to species of Palaemon and Palaemonetes. Finding Macrobrachium to be paraphyletic for the 16S rRNA mitochondrial gene indicates that there are problems within the current morphologically based taxonomy. This position is not new and doubts about the validity of the classification of Macrobrachium have been raised for some time (Boulton and Knott 1986; Fincham 1987). The most widely accepted current classification of Macrobrachium worldwide is that of Holthuis (1950, 1952). However, Holthuis (1952) lists a number of reasons why classification of this genus is made very difficult. These include: a restricted number of characters available for identification, with many features common to all species; the variability of characters within species, especially during the growth of the animal; sexual dimorphism (i.e. morphological differences between males and females of a species); and some species possibly being sexually mature before all body parts are fully developed. A large degree of reliance has been placed on the presence or absence of the hepatic and branchiostegal spines as an indicator of generic boundaries, but it appears, from these results, that this trait may be a primitive feature or simply more plastic than previously realised. Baldwin et al. (1998) and Gusmão et al. (2000) reached a similar conclusion with respect to the unreliability of the morphology of the female thylecum for delineating subgenera within the genus Penaeus. The finding of a

The phylogenetic analyses using the three methods (neighbour joining, ML and MP) resulted in the production of three trees with identical topology (Fig. 1). The two inland species, M. atactum and M. australiense, along with M. rosenbergii form one monophyletic group and Palaemon serenus and M. intermedium form another. Bootstrap confidence levels of 100% support each grouping. Discussion Although only a limited number of species have been sampled, the results of this study are sufficient to indicate inconsistencies within the current classification of Australian Palaemonidae, both at the generic and species level. The hypothesis that the four species of Macrobrachium are monophyletic is clearly unsupported, with M. intermedium and Palaemon serenus forming a well-supported clade distinct from the three other Macrobrachium species. The divergence levels between species from the same genus for the 16S mtDNA gene region in crustaceans is usually between 2% and 17% (e.g. Suno-Ughi et al. 1997; Ponniah and Hughes 1998; Jarman et al. 2000; Tong et al. 2000). Thus, the level of sequence divergence between M. intermedium and P. serenus (0.09 or 9%) is typical of that found between congeneric species, whereas the differences between M. intermedium and the other Macrobrachium species (0.25 or 25%) is more indicative of that normally found between genera. Short (2000), in a review of the taxonomy of Australian Macrobrachium, came to a similar conclusion with regard to the position of M. intermedium,

100

M. atactum M. australiense

100

M. rosenbergii 100

M. intermedium Palaemon serenus Paratya australiensis

Fig. 1. Identical phylogenetic relationships generated by three methods: neighbour joining, maximum likelihood and maximum parsimony. The example shown is the neighbour joining tree; bootstrap values were obtained from 1000 replicates.

700

closer-than-anticipated relationship between M. intermedium and P. serenus is consistent with the fact that they share closely matched distributions and habitats and are similar in body size. Macrobrachium intermedium has also been noted as being abnormal for the genus owing to the lack of sexual dimorphism in the chelipeds, a character normally associated with Macrobrachium (Fincham 1987). There is a possibility that the gene trees generated in this study do not mirror the true phylogenetic relationships among taxa. This is because gene trees derived from mtDNA sequence data may not always be representative of species trees (Brower et al. 1996). However, the large genetic difference between the inland Macrobrachium/M. rosenbergii clade and M. intermedium contrasted with the smaller genetic difference found between Palaemon serenus and M. intermedium provides strong evidence that the relationships shown here reflect evolutionary relationships. The genetic similarity between the two closely related inland species highlights the significance of the greater difference between the inland Macrobrachium species and the estuarine/marine M. intermedium. Another possible cause for the results is the presence of a nuclear copy of the mitochondrial 16S rRNA gene region. Nuclear copies of 16S rRNA have previously been reported in crustaceans (Schneider-Broussard and Neigal 1997). Nuclear copies of mitochondrial genes are known to have different evolutionary characteristics than those of mtDNA, and have been referred to as molecular fossils (Bensasson et al. 2001). Therefore, if a slower evolving nuclear copy of the 16S rRNA gene retaining ancestral characteristics is present in M. intermedium and P. serenus, it is possible that this region may have been amplified instead of the mitochondrial 16S rRNA gene, giving a biased result. Sequencing of a nuclear gene or the use of purified mtDNA for PCR amplifications can verify the absence or presence of translocated mitochondrial DNA. The phylogenetic relationship between M. intermedium and the two inland Macrobrachium species is of special interest, as it may offer some insight into the evolutionary history of Australian members of the genus Macrobrachium. There are two current schools of thought as to how the palaemonids, in particular Macrobrachium, may have arrived in Australia. Bishop (1967) suggested that they most likely originated from Asia and then dispersed throughout eastern Australia, whereas Williams (1981) proposed that they may have evolved relatively recently from in situ marine ancestors. On the basis of these preliminary results, the evolution of Australian Macrobrachium species into inland environments does not appear to have occurred in recent times from extant marine species as suggested by Williams (1981) because M. intermedium is clearly not the ancestor of Australian inland species. Thus, migration southwards from south-east Asian species may be the most likely scenario for their evolution, although the possibility that Australian Macrobrachium

N. P. Murphy and C. M. Austin

species evolved from an older invasion of Australian inland river systems by ancestors of the P. serenus–M. intermedium lineage cannot be excluded. Samples of a range of Asian and Australian species are being analysed to attempt to distinguish between these two hypotheses to explain the radiation of Macrobrachium into Australia. The evolutionary affinities and taxonomic status of Macrobrachium from other continents also requires re-examination given that the group appears to be highly morphologically conservative and features that have been emphasised in classical taxonomic analyses may be less reliable. It is also clear that taxonomic boundaries in other palaemonid genera (e.g. Palaemon and Palaemonetes) need to be examined. The limited genetic distance between the allopatric Macrobrachium australiense and M. atactum also brings into question the reliability of the current species-level classification. Interspecies genetic distance in the 16S rRNA mtDNA gene region for decapod crustaceans usually ranges from 2% to 17%. A genetic distance of under 2% between M. australiense and M. atactum samples 1000 kilometres apart in inland Australia is more consistent with intraspecific rather than interspecific differences. Short (2000) concluded that delimiting M. australiense and M. atactum via morphological means was an impractical task and recommended that M. atactum, along with other species and subspecies described by Riek (1951), be recognised as new junior subjective synonyms of M. australiense. Further molecular genetic investigation into the interrelationships and status of these ‘species’ will help in understanding these relationships and is therefore justified. In conclusion, the current morphologically based classification of Macrobrachium, as well as the Palaemonidae, must be considered under doubt. Although this study has only examined four Macrobrachium species, it has identified inconsistencies in the classification of these shrimps at both the genus and species levels. The worldwide distribution of this genus and the nature of the life cycle (in freshwater or estuarine environments) suggests that it may be a morphologically conservative and relatively ancient group with hidden diversity. This raises some intriguing questions regarding the evolutionary history and biogeography of the group and invites further investigation using molecular genetic data. Acknowledgments N. P. Murphy was supported by an Australian Postgraduate Award. We would like to thank Thuy Nguyen, Lachlan Farrington, Mike Truong, Adam Miller and Paul Jones for assistance in collecting samples. References Baldwin, J. D., Bass, A. L., Bowen, B. W., and Clark, W. H. (1998). Molecular phylogeny and biogeography of the marine shrimp Penaeus. Molecular Phylogenetics and Evolution 10(3), 399–407.

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Manuscript received 17 August 2001; revised and accepted 11 April 2002.

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