Population structure, effective population size and adverse effects of stocking in the endangered Australian eastern freshwater cod Maccullochella ikei

Microsatellite markers were used to examine spatio-temporal genetic variation in the endangered eastern freshwater cod Maccullochella ikei in the Clarence River system, eastern Australia. High levels of population structure were detected. A model-based clustering analysis of multilocus genotypes identified four populations that were highly differentiated by F-statistics (F(ST) = 0·09 - 0·49; P < 0·05), suggesting fragmentation and restricted dispersal particularly among upstream sites. Hatchery breeding programmes were used to re-establish locally extirpated populations and to supplement remnant populations. Bayesian and frequency-based analyses of hatchery fingerling samples provided evidence for population admixture in the hatchery, with the majority of parental stock sourced from distinct upstream sites. Comparison between historical and contemporary wild-caught samples showed a significant loss of heterozygosity (21%) and allelic richness (24%) in the Mann and Nymboida Rivers since the commencement of stocking. Fragmentation may have been a causative factor; however, temporal shifts in allele frequencies suggest swamping with hatchery-produced M. ikei has contributed to the genetic decline in the largest wild population. This study demonstrates the importance of using information on genetic variation and population structure in the management of breeding and stocking programmes, particularly for threatened species.

Rapid ribosomal RNA sequencing and the phylogenetic analysis of protists

A newly described technique for rapidly obtaining the partial nucleotide sequence of ribosomal RNA is being applied to investigate phylogenetic relationships among living organisms. Alan Johnson and Peter Boverstock describe the importance of this method to parasitology in providing new information on the phylogenetic relationships of parasitic organisms previously placed in groups of convenience. The phylum Apicomplexo in particular, has been the object of much study using this technique, but the technology is likely to extend soon to the restructuring of the phylogenetic trees of many groups of parasites.

The phylogenetic relationships of the bilby, Macrotis lagotis (Peramelimorphia: Thylacomyidae), to the bandicoots- DNA sequence evidence

Partial sequencing of the 12S ribosomal RNA gene was used to test two competing hypotheses concerning the phylogenetic relationship of the bilby (Macrotis lagotis) to the Australian and New Guinean species of bandicoot. The first hypothesis proposes that the Australian and New Guinean bandicoots are in a monophyletic clade to the exclusion of the bilbies, whereas the second hypothesis proposes that the bilby is monophyletic with the Australian bandicoots to the exclusion of the New Guinean bandicoots. Phylogenies determined by both maximum-likelihood and neighbour-joining approaches supported the first hypothesis in which the bilby is excluded from the clade represented by the Australian and New Guinean bandicoots. Monophyly of the Australian and New Guinean bandicoots is consistent with the biogeographical scenario in which Australia and Papua New Guinea have undergone repeated connection and disconnection over the last 20 million years.

Phylogenetic relationships of Australian members of the family percichthyidae inferred from mitochondrial 12S rRNA sequence data

Phylogenetic relationships among 20 Australian species of the family Percichthyidae were investigated from sequence data of two portions of the mitochondrial 12S rRNA gene. The molecular data indicate that Australian genera within this family cluster into three distinct clades. The first clade is composed of some species currently ascribed to the genus Macquaria, along with Nannatherina, Nannoperca, and Bostockia, the second of Maccullochella and two catadromous Macquaria species, and the third of Gadopsis. However, the positioning of Gadopsis within this family was unresolved. Monophyly within each genus was well supported, except for Macquaria, which is clearly polyphyletic. The molecular data were used to examine two hypotheses of Australian percichthyid evolution and favor a freshwater origin for the family.

Population genetics of Escherichia coli in a natural population of native Australian rats

Escherichia coli, a normal inhabitant of the intestinal tract of mammals and birds, is a diverse species. Most studies on E. coli populations involve organisms from humans or human-associated animals. In this study, we undertook a survey of E. coli from native Australian mammals, predominantly Rattus tunneyi, living in a relatively pristine environment in the Bundjalung National Park. The genetic diversity was assessed and compared by multilocus enzyme electrophoresis (MLEE), sequence analysis of the mdh (malate dehydrogenase) gene and biotyping using seven sugars. Ninety-nine electrophoretic types were identified from the 242 isolates analysed by MLEE and 15 sequences from the mdh genes sequenced from 21 representative strains. The Bundjalung isolates extend the diversity represented by the E. coli reference (ECOR) set, with new MLEE alleles found in six out of 10 loci. Many of the Bundjalung isolates fell into a discrete group in MLEE. Other Bundjalung strains fell into the recognized E. coli ECOR set groups, but tended to be at the base of both the MLEE and mdh gene trees, implying that these strains are derived independently from ancestral forms of the ECOR groups and that ECOR strains represent only a subset of E. coli adapted to humans and human-associated animals. Linkage disequilibrium analysis showed that the Bundjalung population has an 'epidemic' population structure. The Bundjalung isolates were able to utilize more sugars than the ECOR strains, suggesting that diet plays a prominent role in adaptation of E. coli.

Evolutionary lineages of RT1.Ba in the Australian Rattus

In this study, the evolutionary history of the variable second exon of RT1.Ba and its adjoining intron b are compared across a number of species and subspecies of the Australian RATTUS: Three lineages are identified in the second intron across a range of Rattus species. Two of these lineages, separated by the insertion of a probable rodent short interspersed nucleotide element and by point mutations outside the indel region, are both found in each of the major clades of the endemic Australian RATTUS: This pattern of ancestral polymorphism is reflected in the adjoining exon 2 sequences, although phylogenetic constraints confirm that the clustering is not identical to that of the associated intron sequences. In addition, the coding sequences show evidence of the retention of ancestral polymorphism, with identical exon sequences found in two divergent species, and some indication of gene conversion detected for the exon sequences.

Variation on islands: major histocompatibility complex (Mhc) polymorphism in populations of the Australian bush rat

Loss of genetic variation in small, isolated populations is commonly observed at neutral or nearly neutral loci. In this study, the loss of genetic variation was assessed in island populations for a locus of major histocompatibility complex (Mhc), a locus shown to be under the influence of balancing selection. A total of 36 alleles was found at the second exon of RT1.Ba in 14 island and two mainland populations of Rattus fuscipes greyii. Despite this high overall diversity, a substantial lack of variation was observed in the small island populations, with 13 islands supporting only one to two alleles. Two populations, Waldegrave and Williams Islands, showed moderately high levels of heterozygosity (52-56%) which were greater than expected under neutrality, suggesting the action of balancing selection. However, congruence between the level of variation at this Mhc locus and in previous allozyme electrophoresis and mitochondrial DNA studies highlights the dominant influence of genetic drift and population factors, such as bottlenecks and structuring in the founding population, in the loss of genetic variation in these small, isolated populations.

Phylogeographic differentiation in the mitochondrial control region in the koala, Phascolarctos cinereus (Goldfuss 1817)

The koala, Phascolarctos cinereus, is a geographically widespread species endemic to Australia, with three currently recognized subspecies: P.c. adustus, P.c. cinereus, and P.c. victor. Intraspecific variation in the mitochondrial DNA (mtDNA) control region was examined in over 200 animals from 16 representative populations throughout the species' range. Eighteen different haplotypes were defined in the approximately 860 bp mtDNA control region, as determined by heteroduplex analysis/temperature gradient gel electrophoresis (HDA/TGGE). Any single population typically possessed only one or two haplotypes yielding an average within-population haplotypic diversity of 0.180 +/- 0.003, and nucleotide diversity of 0.16%. Overall, mtDNA control region sequence diversity between populations averaged 0.67%, and ranged from 0% to 1.56%. Nucleotide divergence between populations averaged 0.51%, and ranged from 0% to 1.53%. Neighbour-joining methods revealed limited phylogenetic distinction between geographically distant populations of koalas, and tentative support for a single evolutionarily significant unit (ESU). This is consistent with previous suggestions that the morphological differences formalized by subspecific taxonomy may be interpreted as clinal variation. Significant differentiation in mtDNA-haplotype frequencies between localities suggested that little gene flow currently exists among populations. When combined with microsatellite analysis, which has revealed substantial differentiation among koala populations, we conclude that the appropriate short-term management unit (MU) for koalas is the local population.

Microsatellite variation and assessment of genetic structure in tea tree (Melaleuca alternifolia-Myrtaceae)

Analysis of five microsatellite loci in 500 Melaleuca alternifolia individuals produced 98 alleles that were useful for population genetic studies. Considerable levels of observed heterozygosity were recorded (HO = 0.724), with approximately 90% of the variability being detected within populations. A low level of selfing (14%) was suggested to be the principal cause of excess homozygosity in a number of populations (overall FIS = 0.073). This study showed low levels of inbreeding in certain populations as well as a significant isolation-by-distance model. Only two groups of populations (Queensland and New South Wales) constituted different genetic provenances as a result of geographical isolation. The M. alternifolia data suggest that microsatellite loci did not always arise by a stepwise mutation process but that larger jumps in allele size may be involved in their evolution.

Consequences of a catadromous life-strategy for levels of mitochondrial DNA differentiation among populations of the Australian bass, Macquaria novemaculeata

The influence of a catadromous life-strategy on levels of spatial genetic structuring in fish is poorly understood. In an effort to gain a better appreciation of how this specialized life-strategy determines population genetic structuring, we assessed variation in the mitochondrial DNA (mtDNA) control region in a catadromous perciform, the Australian bass Macquaria novemaculeata. Nineteen putative haplotypes were resolved using temperature gradient gel electrophoresis from 10 geographically distinct populations. Significant heterogeneity was revealed in haplotype frequencies and their spatial distributions among many locales. Gene partitioning statistics (AMOVA) for both raw haplotype frequency data and frequency data with sequence divergences were concordant, indicating that M. novemaculeata populations were moderately genetically structured (phi ST = 0.05, 0.06; P < 0.001, respectively). Isolation by distance seems to be a strong structuring force in M. novemaculeata, culminating in no detectable phylogeographic structuring among haplotypes. Low sequence divergences were observed among many haplotypes and it is suggested that these are the result of pruning of maternal lineages by cyclical variations in female reproductive success. This study highlights the importance of life-history patterns and, in particular, spawning locality, in determining spatial structuring of mtDNA variation in catadromous species.

The rate of mitochondrial 12S rRNA gene evolution is similar in freshwater turtles and marsupials

Assertions that the "conventional" rate of mitochondrial DNA (mtDNA) evolution is reduced in poikilotherms in general and turtles in particular were tested for side-necked turtles (Pleurodira: Chelidae). Homologous data sets of mitochondrial 12S rRNA gene sequences were used to compare the average divergence between the Australian and South American species for two Gondwanan groups: the chelid turtles and the marsupials. The mean nucleotide divergences between continental groups for both the turtles and the marsupials are remarkably similar. These data suggest that the rate of evolution of mitochondrial 12S rRNA gene is not substantially slower in turtles than in the homeothermic marsupials.

Myoglobin intron variation in the Gouldian Finch Erythrura gouldiae assessed by temperature gradient gel electrophoresis

In this study we show how the use of exon-primed, intron-crossing (EPIC) polymerase chain reaction (PCR) of a diploid intronic region, in conjunction with temperature gradient gel electrophoresis (TGGE), can be used to detect and rapidly assess allelic variation at the nucleotide level. We developed passerine-specific primers to amplify and sequence a 762 bp region including the second intron of the myoglobin gene in the Gouldian Finch, Erythrura gouldiae. A POLAND plot based on this sequence indicated that TGGE in combination with heteroduplex analysis (TGGE/HA) should reveal nucleotide variation in the 160 bp low-melting domain. Sequencing of the entire fragment from 19 Er. gouldiae revealed five nucleotide substitution differences within the low-melt domain, all of which could be detected and differentiated by TGGE/HA, and an additional substitution in a section of the high-melt domain which characterised another allele. A total of 181 individuals from four populations were screened for these six alleles.

The Thevenard Island mouse: historic and conservation implications from mitochondrial DNA sequence-variation

The level of mitochondrial differentiation between Thevenard Island and mainland populations of the short-tailed mice Leggadina lakedownensis was determined using DNA sequencing of the Control Region. Using temperature gradient gel electrophoresis, outgroup heteroduplex analysis detected eight haplotypes. These were sequenced for 362 basepairs. Our results show that the Thevenard Island Short-tailed Mouse is indeed L. lakedownensis, and is most closely related to L. lakedownensis in the Pilbara in Western Australia. Together, Thevenard Island and adjacent mainland populations are sufficiently divergent from those in northern Australia as to be recognized as two clearly distinct mitochondrial DNA lineages. Conservation and taxonomic implications arising from a phylogeny of haplotypes suggest that two Management Units exist within L. lakedownensis ? a northern unit that includes individuals from the Kimberley (Western Australia) to Kakadu National Park (Northern Territory), and a western unit comprising individuals from Thevenard Island and the Pilbara (Western Australia). These conservation units should be managed as separate subspecies of L. lakedownensis, and a high conservation priority should be given to the Thevenard Island population because it provides an important refugium for L. lakedownensis not just in the Pilbara, but in Australia.

Phylogenetic relationships of chelid turtles (Pleurodira: Chelidae) based on mitochondrial 12S rRNA gene sequence variation

Conflicting phylogenies have been proposed for the Chelidae (Testudines: Pleurodira), a family of side-necked turtles found only in Australasia and South America. Sequence data from the mitochondrial 12S rRNA gene were used to test these phylogenies. In total, 411 nucleotides were sequenced for each of 16 chelid species, including all 11 recognized chelid genera and, as outgroups, 5 genera of Pelomedusidae (Testudines: Pleurodira). Analyses using parsimony and neighbor joining algorithms strongly support the division of Australian Chelidae into the three monophyletic groups initially suggested by Burbidge et al. (1974; Copeia 2: 392-409): Chelodina (bootstrap value 99%), the Emydura group (87%), and Pseudemydura. The analyses suggest that the Australian chelids are a monophyletic lineage (64%), with the Australian long-necked turtles, Chelodina, more closely related to the Australian short-necked chelids than to the long-necked South American species. These relationships are in contrast to those of Gaffney (1977; Am. Mus. Novitates 2620: 1-28). The species of Australian long-necked chelids consistently form a monophyletic clade, with Chelodina longicollis and Chelodina oblonga as sister taxa. The data failed to resolve relationships among the Australian short-necked taxa: Emydura, the Elseya latisternum group, the Elseya dentata group, Rheodytes, and Elusor. Unlike Gaffney (1977), we find some weak support (58%) for Pseudemydura as the closest relative of the other Australian short-necked taxa. With the exception of Hydromedusa, the South American taxa are monophyletic and the subgenera of Phrynops are paraphyletic.

Preliminary investigation of nocturnal habitat use by migratory waders (Order Charadriformes) in northern New South Wales

Nocturnal and diurnal habitat use by migrant waders was studied at three sites in the Richmond estuary, northern New South Wales. Numerous species of migrant wader showed significant differences in habitat use between night and day. Sanderling (Calidris alba), red-necked stint (Calidris ruficollis) and, possibly, double-banded plover (Charadrius bicinctus) foraged on mudflats during the day but moved to ocean beaches to forage during night low tides. Pacific golden plover (Pluvialis fulva), greater sandplover (Charadrius leschenaultii), eastern curlew (Numenius madagascariensis) and bar-tailed godwit (Limosa lapponica) displayed less significant differences in habitat use, although densities increased at night on moist sandy mudflats. The numbers of terek sandpiper (Xenus cinereus) and curlew sandpiper (Calidris ferruginea) decreased on sandy mudflats at night although where these birds went is unknown. Nocturnal foraging by X. cinereus may be restricted to moonlit nights. Greenshank (Tringa nebularia) also displayed differences in habitat use by foraging more on moist sandy mud at night and less in sea grass. No significant differences were found for whimbrel (Numenius phaeopus). Habitat use by both N. madagascariensis and N. phaeopus appears related to lunar phase. Six hypotheses are postulated to explain the observed differences: (1) exploitation of changes in prey behaviour and availability; (2) predator avoidance; (3) human avoidance; (4) increased light on mudflats from urban areas; (5) avoidance of roosting flocks of gulls and terns; and (6) relationship with prevailing environmental conditions. The data presented provide a basis from which further work will be undertaken.

Outgroup heteroduplex analysis using temperature gradient gel electrophoresis: high resolution, large scale, screening of DNA variation in the mitochondrial control region

The ability of DNA screening techniques such as Temperature Gradient Gel Electrophoresis (TGGE) and Heteroduplex Analysis to provide resolution approaching that provided by DNA sequencing for a fraction of the time, effort and expense point to them as the logical successor to allozyme electrophoresis for population genetics. Here we present a novel alternative to the standard TGGE/Heteroduplex Analysis protocol - Outgroup Heteroduplex Analysis (OHA). We assess this technique's sensitivity in comparison to previous screening approaches using a known hierarchy of sequence differences. Our data show that Outgroup Heteroduplex Analysis has greatly increased sensitivity for screening DNA variants from that of TGGE used alone and is easily applicable to large numbers of samples. Using this technique we can consistently detect differences of as small as one base change in a 433-base-pair fragment of Control Region mitochondrial DNA from Melomys cervinipes (an Australian rodent). The approach should easily be extendable to nuclear loci and is not necessarily dependent on the use of a denaturing gradient. When combined with a targeted sequencing effort, OHA provides a sensitive and simple means of obtaining allele/haplotype frequencies and their phylogenies for population and phylogeographic studies in molecular ecology.

Phylogenetic relationships between Toxoplasma and Sarcocystis deduced from a comparison of 18S rDNA sequences

The current taxonomy of parasites in the genus Sarcocystis is largely based on morphological characteristics as well as on host specificity and life-cycle structure. Recently, phylogenetic analyses of partial ribosomal RNA (rRNA) sequences provided support for paraphyly of Sarcocystis. We have tested the validity of this hypothesis by sequencing the complete 18S rRNA genes of Sarcocystis arieticanis, Sarcocystis gigantea and Sarcocystis tenella and comparing them with gene sequences derived from other taxa of the phylum Apicomplexa. The results obtained from this study do not reject the hypothesis of monophyly of Sarcocystis species, although the bootstrap data were inconclusive for some species.

Evolution in the Murinae (Rodentia) Assessed by Microcomplement Fixation of Albumin

The inter-relationship of 17 genera of Murinae rodents were studied using microcomplement fixation of albumin to measure immunological distances among taxa. The genera chosen represented six major clades and four monogeneric groups identified in earlier companion studies (an African group, a South-east Asian group, a New Guinean group, an Australasian group, an Acomys group, a Micromys group and Apodemus, Millardia, Mus and Phloeomys). When these companion studies are included 136 species and 67 genera were studied. Ten major clades were consistently supported by the data but apart from linking the South-east Asian and Australasian clades, the data do not resolve their inter-relationships. The Acomys-Uranomys-Lophouromys clade may be the sister-group to the rest of the Murinae. Otomys (Otomyinae) is considered to be a murine related to the African group of genera. Of the ten major clades identified, only one (Mus) occurs significantly in more than one primary biogeographic region. It is suggested that following an early period of relatively rapid dispersal from the place of origin, little further dispersal took place and subsequent evolution occurred within relatively confined geographic areas.

The phylogenetic relationships of Kronborgia (Platyhelminthes, Fecampiida) based on comparison of 18S ribosomal DNA sequences

Approximately 580 bp at the 5' end of the small subunit RNA gene were amplified by PCR for 19 platyhelminth taxa, and Homo and Artemia were used as outgroups. These were analysed to test the hypothesis that fecampiids and Neodermata are sister groups. No evidence was found that the fecampiid Kronborgia isopodicola is closely related to the Neodermata or to the Rhabdocoela (in which the fecampiids are usually included). Morphological, including ultrastructural, characters and DNA data do not support a close relationship of fecampiids with any other platyhelminth taxon, although the DNA sequence analysis provides some evidence that the Acoela and Tricladida are closest. Fecampiids are sufficiently different from any other platyhelminth group to warrant establishment of a class, Fecampiida, for them. A diagnosis of the new class is given.

The phylogeny of Neospora caninum

Morphological studies by electron microscopy on the protozoan Neospora caninum have shown that this organism possesses a subcellular structure typical of parasites classified in the family Sarcocystidae, subclass Coccidiasina of the phylum Apicomplexa. Using a strategy based on DNA sequence analysis of products derived by asymmetric PCR to determine the nucleotide sequences, we have tested the validity of this classification by comparing the small subunit ribosomal RNA (18S rRNA) gene sequences of N. caninum with those of other parasitic protozoa classified in the phylum Apicomplexa. The results of this analysis confirm the placing of N. caninum in the family Sarcocystidae and place it as a sister group to Toxoplasma gondii in the phylum Apicomplexa.

Evolution in New-Guinean Muridae (Rodentia) Assessed by Microcomplement Fixation of Albumin

The interrelationships of 19 genera and 28 species of New Guinean rodents representing 80% of the currently recognised New Guinean genera, were studied using microcomplement fixation of albumin to measure immunological distances among genera. The phylogenetic distinctiveness of Rattus and the closely related Stenomys from all other genera was confirmed. The remaining genera fall into three groups: (i) Lorentzimys; (ii) Anisomys, Coccymys, Chiruromys, Hyomys, Macruromys, Mallomys and Pogonomys; and (iii) Crossomys, Hydromys, Leptomys, Mayermys, Melomys, Neohydromys, Parahydromys, Pseudohydromys and Uromys. Solomys, from the Solomon islands, and Leggadina, Mesembriomys and Xeromys, from Australia, were shown to belong to this latter group. Groups (i) and (ii) are essentially endemic to New Guinea, while the third shares genera and species with Australia.

Evolution in Some South-East Asian Murinae (Rodentia), as Assessed by Microcomplement Fixation of Albumin, and Their Relationship to Australian Murines

The interrelationships of 16 genera and 49 species of predominantly South-east Asian murine rodents were studied by means of microcomplement fixation of albumin to measure immunological distances among taxa. The results are viewed as a hypothesis of the phylogenetic relationship of these taxa that can be tested by other data sets. Three main groupings are suggested: (1) Maxomys; (2) Leopoldomys, Niviventer and Tokudaia; and (3) Bandicota, Berylmys, Bullimus, Bunomys, Komodomys, Nesokia, Papagomys, Paruromys, Rattus, Stenomys, Sundamys and Taeromys. Within this latter group, Bunomys chrsogasta, Komodomys and Rattus timorensis group together, as do Bullimus, Rattus and Stenomys, and Bandicota with Nesokia. The Australian murines, represented by Mesembriomys, may be part of this South-east Asian radiation but, if so, arose early in its history. Biogeographically, the results support South-east Asia as being a centre of murine evolution with secondary foci in Sulawesi, New Guinea and Australia. There is some evidence to suggest that a relatively recent land bridge between Sulawesi, Flores and Timor may have existed.

Contributions to the phylogeny of Platyhelminthes based on partial sequencing of 18S ribosomal DNA

Partial sequencing of the 18S ribosomal DNA gene of one nemertean and 13 free-living and parasitic Platyhelminthes (556 nucleotides), and of one nemertean and 20 Platyhelminthes (556 nucleotides) was used to test several hypotheses concerning the phylogenetic relationships of Platyhelminthes. The following conclusions were reached: the Neodermata is monophyletic; Trematoda (Aspidogastrea and Digenea) is monophyletic, although a sister group relationship of the Aspidogastrea and all other Neodermata cannot be definitely ruled out; the Cestoda comprising the Eucestoda, Amphilinidea and Gyrocotylidea is monophyletic; it is unresolved whether the Monogenea is paraphyletic; neither Gyrocotylidea and Monopisthocotylea nor Gyrocotylidea and Monogenea as a whole are sister groups; Anoplodiscus is a monopisthocotylean monogenean; none of Proseriata, Pterastericolidae/Umagillidae, Kalyptorhynchia, Rhabdocoela as a whole, Dalyelliida or the Temnocephalidae is the sister group of the Neodermata; there is some evidence that a larger taxon consisting of Proseriata, Tricladida and Rhabdocoela may be the sister group of the Neodermata but definitive evidence for a sister group relationship between the Neodermata and any turbellarian taxon is lacking; Rhabdocoela and Lecithoepitheliata are not closely related; it is unresolved whether the Rhabdocoela is monophyletic; Umagillidae, Pterastericolidae and Temnocephalidae belong to one monophylum; the Temnocephalidae are very close to the dalyelliids; Tricladida and Rhabdocoela are sister groups, the exact position of the Catenulida and Nemertini in relation to the Platyhelminthes has not been resolved, although Catenulida and Lecithoepitheliata may belong to one clade.

Phylogenetic relationships of the thylacine (Mammalia: Thylacinidae) among dasyuroid marsupials: evidence from cytochrome b DNA sequences

DNA sequences from the mitochondrial cytochrome b gene were obtained from a museum specimen of the presumed extinct thylacine (Thylacinus cynocephalus) and were compared with homologous sequences from 13 representatives of the Australian marsupial family Dasyuridae. The relationship of the thylacine to dasyurids has been suggested by previous anatomical and molecular studies, but its position within the dasyuroid radiation has not been addressed with genetic data. Phylogenetic analysis of the sequences reported here suggests that the thylacine is a sister group to Dasyuridae and lends support to the hypothesis that Thylacinus represents an ancient Australian marsupial lineage. Relationships with Dasyuridae support the results of other recent molecular studies, particularly in showing the affinities of endemic New Guinean subfamilies with larger Australian clades.

The Evolution of Species of the Varanidae - Microcomplement Fixation Analysis of Serum Albumins

Phylogenetic relationships among 30 of the 40 species in the Varanidae were examined in the light of molecular information on albumin evolution derived from microcomplement fixation. A phylogeny based on these results is compared with proposed phylogenies based on data obtained using other techniques. Three separate radiations of Varanus are found in Australia, The movement of varanids to Australia from south-east Asia is thought to have occurred approximately 15-20 million years ago.

Ribosomal DNA sequence comparison of Babesia and Theileria

Previous studies on the taxonomy of Babesia spp. (phylum Apicomplexa) using morphological and life cycle characteristics have resulted in their classification into 3 subgenera, with the genus Theileria being most closely related to them. Using a strategy based on the direct sequence analysis of products derived by asymmetric PCR to determine the nucleotide sequences, we have tested the validity of this classification by sequencing the small subunit ribosomal RNA genes amplified from 2 Babesia species, namely Babesia bovis and Babesia rodhaini, and comparing these with previously published sequences of Theileria annulata and Babesia bigemina using Plasmodium falciparum as an outgroup. The results of this phylogenetic analysis support the recognition of at least 2 genera in Babesia--one to include B. bigemina and B. bovis, the other to include B. rodhaini.

Phylogenetic relationships of Sarcocystis species from sheep, goats, cattle and mice based on ribosomal RNA sequences

Partial sequences of the small subunit ribosomal RNA of four species of Sarcocystis were obtained by reverse transcription of total cellular RNA. The semi-conserved regions of these four species were aligned with homologous sequences of two other Sarcocystis species and a range of other eukaryotes including Toxoplasma, Eimeria and Cryptosporidium. Parsimony analysis of the aligned sequences showed that Sarcocystis and Toxoplasma had a more recent common ancestor with Eimeria than with Cryptosporidium. The six Sarcocystis spp. did not cluster together in this analysis; two monophyletic groups were observed, one formed by the two Sarcocystis spp. with felids as definitive hosts, and another by the four Sarcocystis spp. with canids as definitive hosts. These two clades were segregated by Toxoplasma. An analysis of nucleotide divergence suggests that the difference between the two groups of Sarcocystis spp. is similar to that between invertebrates and vertebrates. The results obtained here question the validity of a separation of the genus Sarcocystis from Toxoplasma and refute classifications that place these two genera into two different subfamilies of the Sarcocystidae.

Phylogeny of the Australian Rodents (Muridae) - a Molecular Approach Using Microcomplement Fixation of Albumin

Microcomplement fixation was used to assess albumin evolution in the history of the rodents of Australia. The results confirmed a monophyletic grouping consisting of the genera Pseudomys, Mastacomys and Notomys, and showed that the genus Pseudomys is paraphyletic. The genera Conilurus, Leporillus and Mesembriomys also formed a monophyletic group. A significant finding was that Leggadina was distantly related to all Pseudomys species, and indeed may be the earliest offshoot of all Australian rodents other than Rattus. Albumin evolution in the Australian rodents has occurred in a manner far from clock-like. Mastacomys Thomas, 1882 is synonymised with Pseudomys Gray, 1832.

Rates of Albumin Evolution in Parrots (Aves, Psittaciformes)

A number of lines of evidence suggest that the rate of molecular evolution in birds is slower than in other vertebrates. This hypothesis was tested by measuring the extent of amino-acid sequence divergence in albumin among species of parrots by means of microcomplement fixation. This group was chosen because its modern distribution is strongly suggestive of a Gondwanan origin. The results show that the intercontinental albumin distances are well below those expected for a Gondwanan group. These data are in accord with the hypothesis that birds have a slower rate of molecular evolution, although other explanations are possible.

Evolutionary Relationships of the Australasian Mud-Nesters (Grallinidae, Corcoracidae) - Immunological Evidence

The phylogenetic relationships of the genera of Australasian mud-nesters (Corcorax, Struthidea and Grallina) were examined by microcomplement fixation, and the results compared with morphological and DNA-DNA hybridisation data. There was general corroboration among all data sets such that (1) Corcorax and Struthidea were well-diverged members of a single lineage related to corvoids, and (2) Grallina comprised two species (Australian G. cyanoleuca and New Guinean G. bruijni) closely allied to Myiagra among the monarch flycatchers (Monarchidae). The immunological data also indicated that Corcorax and Struthidea were closer to Corvus (Corvinae) than to some other members of that subfamily identified by DNA-DNA hybridisation. There was further corroboration of evidence from DNA-DNA hybridisation for an endemic radiation among Australo-Papuan passerine families.

Conflicting phylogenetic hypotheses for the parasitic platyhelminths tested by partial sequencing of 18S ribosomal RNA

Partial sequencing of the 18S ribosomal RNA in nine parasitic and one free-living species of platyhelminth was used to test hypotheses on the phylogenetic relationships among the major groups. The eucestodes, amphilinideans, gyrocotylideans and monopisthocotylideans appeared as a monophyletic assemblage in a cladistic analysis of the data, with a very close association between the gyrocotylideans and monopisthocotylideans. The polyopisthocotylidean monogeneans were paraphyletic to the monopisthocotylideans. The digeneans appeared to be a sister group to the monogeneans and eucestodes, while the temnocephalidean was closely related to the free-living polyclad.

A Phylogenetic Comparison of 18s-Ribosomal Rna Sequences of Lungfish With Those of Other Chordates

A rapid RNA-sequencing technique was used to partially sequence the 18S ribosomal RNA of species representing seven taxa: Holocephali, Cladistia, Chondrostei, Holostei, Dipnoi, Anura and Caudata. Phylogenetic analysis of the nucleotide sequences strongly suggests that both the Holocephali and Cladistia, and the Anura and Caudata, are each monophyletic groups. There is a weaker suggestion that the Chondrostei and Holostei are monophyletic. The Dipnoi did not group with any one of these more than with any other.

Evolution of the Small Subunit Ribosomal-Rna in Higher Vertebrates

The potential value of rapid sequencing of the srRNA molecule for phylogenetic reconstruction of the higher vertebrates was investigated. The study involved partial sequencing of 19 taxa that, along with 6 sequences from the literature, covered all of the major groups of higher vertebrates. The results show that sequencing of the srRNA molecule is not suitable at this taxonomic level because: (i) there is insufficient nucleotide sequence variation; (ii) expansion segments, although common, have a high probability of convergence for both their position and their sequence; and (iii) the phylogenetic branching of the higher vertebrates has been mainly 'bush-like' rather than 'tree-like'.

Immunological Evolution of Albumin in the Estrildine Finches (Aves, Passeriformes) Is Far From Clock-Like

On the basis of microcomplement fixation studies, the finch Taeniopygia guttata has an albumin whose immunological properties are very different from those of other finches. Outgroup analysis, microcomplement fixation of transferrin, and electrophoretic behaviour of finch albumin, together with phylogenetic considerations based upon chromosomes and allozymes, revealed that the difference is due to rapid change in the immunological properties of T. guttata albumin rather than to a distant relationship of T. guttata to other finches. Indeed, the immunological properties of the albumin of T. guttata has undergone about 15 times as much change as would be expected for an albumin clock. The results highlight the caution that should be exercised when applying the molecular clock ad hoc to immunological data.

Small subunit ribosomal RNA evolution in the genus Acanthamoeba

Reverse transcription of small subunit ribosomal RNA (srRNA) was used to determine the partial nucleotide sequences of the srRNA of seven isolates of Acanthamoeba. These seven sequences and the sequence of the corresponding region in an A. castellanii previously totally sequenced were compared in order to investigate evolution of the srRNA gene in Acanthamoeba. The results of the comparisons were consistent with the hypotheses that the genus is monophyletic, that the Pussard and Pons grouping system is valid, that the Acanthamoeba expansion segments in the srRNA gene evolve at a much faster rate than the rest of the gene, and that the extent of nucleotide sequence divergence in the genus Acanthamoeba is roughly similar to that differentiating vertebrates and invertebrates.

Phylogenetic relationships of Cryptosporidium determined by ribosomal RNA sequence comparison

Reverse transcription of total cellular RNA was used to obtain a partial sequence of the small subunit ribosomal RNA of Cryptosporidium, a protist currently placed in the phylum Apicomplexa. The semi-conserved regions were aligned with homologous sequences in a range of other eukaryotes, and the evolutionary relationships of Cryptosporidium were determined by two different methods of phylogenetic analysis. The prokaryotes Escherichia coli and Halobacterium cuti were included as outgroups. The results do not show an especially close relationship of Cryptosporidium to other members of the phylum Apicomplexa.

Immunological Relationships and Generic Revision of the Australian Lizards Assigned to the Genus Leiolopisma (Scincidae, Lygosominae)

The phylogenetic relationships of the Australian scincid lizards currently assigned to the genus Leiolopisma have been examined by quantitative micro-complement fixation (MC'F) comparisons of serum albumin. The results of these comparisons do not support the monophyly implicit in these species' current congeneric status, but suggest instead that the Australian species of Leiolopisma belong to several distinct phyletic lineages within the Eugongylus group. These findings are supported by several sets of non-biochemical characters, including features of scalation, osteology and karyotype. None of the Australian species shares a close relationship with the type-species of Leiolopisrna (L. telfairii), and so a new taxonomic arrangement is proposed which distributes them among the following genera: Bartleia, gen. nov. (jigurru); Bassiana, gen. nov. (duperreyi, platynotum and trilineata); Cautula, gen. nov. (zia); Niveoscincus, gen. nov. (coventryi, greeni, metallicus, microlepidotus, ocellatus, orocryptus, palfreymani and pretiosus); and Pseudemoia Fuhn, 1967 (baudini, entrecasteauxii Group 1; entrecasteauxii Group 2, rawlinsoni and spenceri). Preliminary comparisons suggest that other Leiolopisma species, from New Caledonia, Lord Howe I. and New Zealand, belong to phyletic lineages which are distinct from any of the Australian 'Leiolopisma' and from the type-species.

Albumin Immunological Relationships of Australian Marsupials. 2. The Pseudocheiridae

Microcomplement fixation of albumin was used to examine the phylogenetic relationships among the ringtail possums, family Pseudocheiridae. Phylogenetic analysis of the data supports the hypothesis of at least three distinct clades within the family: one containing Petauroides and Hemibelideus; a second consisting of Pseudocheirus herbertensis, Ps. forbesi, Ps. mayeri, and Ps. canescens; and a third containing Ps. archeri, Ps. corinnae, Ps. cupreus and Ps. dahli. The data have not resolved the phylogenetic position of Ps. peregrinus, which may either form a separate clade or lie close to the Ps. archeri clade.

The Chromosomes of 4 Genera of Possums From the Family Petauridae (Marsupialia, Diprotodonta)

The standard and C-banded (four species) karyotypes of six species of the family Petauridae (Gymnobelideus leadbeateri, Petaurus australis, P. breviceps, P. norfolcensis, Dactylopsila trivirgata and Dactylonax palpator) are described. The G-banded karyotype of P. norfolcensis is also described. Gymnobelideus and Petaurus have diploid chromosome number of 22. All three species of Petaurus have a similar karyotype, consisting of biarmed autosomes and very small sex chromosomes, which differs from Gymnobelideus by a minimum of one chromosomal rearrangement of each autosome. Dactylopsila and Dactylonax have similar karyotypes with diploid chromosome numbers of 18. The relationship of these two genera to Petaurus is still uncertain but all members of this family differ from Pseudocheiridae in the small size of the sex chromosomes.

A genetic approach to species criteria in the amoeba genus Naegleria using allozyme electrophoresis

The present study employs allozyme electrophoresis to characterize and inter-relate 61 isolates of Naegleria. Diploidy was confirmed, with heterozygotes observed at 29 of the 33 loci established and in all but two isolates. With a single exception, isolates clustered at two levels of similarity, either below 21% or above 52%. It is argued that such a major discontinuity provides a sound biological basis for a species concept in Naegleria. On this basis the present species-level taxonomy does not reflect the genetic diversity of the genus. The study recognized 18 genetic groups of species rank. The subspecies N. australiensis italica deserves specific rank; additional thermophilic species not closely related to N. fowleri and N. lovaniensis are recognized; and N. gruberi as currently conceived is a complex of 10 species, at least five of which are represented in the formal culture collections. Most species are genetically too different for relationships to be elucidated by allozyme electrophoresis, supporting the view that some of the times of divergence within the genus are extremely ancient.

Genetic characterization of three strains of Hymenolepis diminuta at 39 enzyme loci

The technique of allozyme electrophoresis was applied to three strains of Hymenolepis diminuta to distinguish between three hypotheses [(1) multiple species, (2) genetically distinct founder stocks and (3) response to differential selection among similar stocks] proposed to account for metabolic differences among strains. There was no evidence from the 39 enzyme loci established that the three strains represented more than one species. In the absence of knowledge of the population structure of H. diminuta in the wild, electrophoretic data herein could not distinguish between the latter hypotheses. Nevertheless, all three strains were distinguishable on electrophoretic profiles and allelic similarities between strains question the view of their proposed origins.

Genetic characterization of three species of Onchocerca at 23 enzyme loci

The technique of allozyme electrophoresis was applied to species of Onchocerca from cattle to increase the number of enzyme loci established and therefore provide a genetic basis for a rational species-level taxonomy. Twenty-three enzyme loci were established and provided unequivocal genetic evidence for the taxonomic validity of Onchocerca gibsoni, O. gutturosa and O. lienalis. Furthermore, the diagnostic enzyme markers detected form the basis for identification of life-cycle stages, individuals and species and population structure analyses.

srRNA evolution and phylogenetic relationships of the genus Naegleria (Protista: Rhizopoda)

A rapid RNA sequencing technique was used to partially sequence the small-subunit ribosomal RNA (srRNA) of four species of the amoeboid genus Naegleria. The extent of nucleotide sequence divergence between the two most divergent species was roughly similar to that found between mammals and frogs. However, the pattern of variation among the Naegleria species was quite different from that found for those species of tetrapods characterized to date. A phylogenetic analysis of the consensus Naegleria sequence showed that Naegleria was not monophyletic with either Acanthamoeba castellanii or Dictyostelium discoideum, two other amoebas for which sequences were available. It was shown that the semiconserved regions of the srRNA molecule evolve in a clocklike fashion and that the clock is time dependent rather than generation dependent.