Recovery of saltwater crocodiles following unregulated hunting in tidal rivers of the Northern Territory,Australia

Saltwater crocodiles (Crocodylus porosus) in the Northern Territory of Australia were protected in 1971, after a severe population decline resulting from 26 yr of intense commercial hunting. By that time wild saltwater crocodiles were rarely sighted anywhere and they were commercially extinct in areas where they had once been abundant. Standardized monitoring by spotlight surveys started in 1975 and provided relative density indices over time (1975–2009) as a unique record of the post-protection recovery of a wild crocodilian population. We examined the survey data for populations at 12 major tidal rivers, individually and as a single subpopulation. The pattern of recovery in the subpopulation in both abundance and biomass was approximated by logistic curves, predicting 5.26 non-hatchling crocodiles weighing 387.64 kg sighted per kilometer of river in 2010. We predicted potential carrying capacity as 5.58 non-hatchling crocodiles (5.73% higher than 2010) weighing 519.0 kg (25.31% higher than 2010). Individual rivers showed largely different abundance and biomass among rivers. The statistical model that best described the recovery in individual rivers was not always logistic. However, where it was logistic, expected carrying capacity of different rivers showed considerable variation in abundance and biomass. The variation indicates different habitat quality among the rivers. Recovery occurred despite various consumptive uses, particularly a widespread egg-harvest program, which has been an integral part of the incentive-driven conservation program for saltwater crocodiles in the Northern Territory since 1983. We suggest that the saltwater crocodile population of the Northern Territory is achieving full recovery from uncontrolled hunting in 1945–1971. Although saltwater crocodiles are considered an important natural resource, their increase in number, size, and distribution is posing management issues for public safety. Continuation of human–crocodile conflict management through public education and strategic removal of problem crocodiles will be essential. © 2011 The Wildlife Society.     

253 Novel polymorphic microsatellites for the saltwater crocodile (Crocodylus porosus)

Genomic elucidation and mapping of novel organisms requires the generation of large genetic resources. In this study, 253 novel and polymorphic microsatellite loci were isolated and characterized for the saltwater crocodile (Crocodylus porosus) by constructing libraries enriched for microsatellite DNA. All markers were evaluated on animals obtained from Darwin Crocodile Farm in the Northern Territory, Australia, and are intended for future use in the construction of a genetic-linkage map for the saltwater crocodile. The 253 loci yielded an average of 4.12 alleles per locus, and those selected for mapping had an average polymorphic information content (PIC) of 0.425.     

Body size drives allochthony in food webs of tropical rivers

Food web subsidies from external sources (“allochthony”) can support rich biological diversity and high secondary and tertiary production in aquatic systems, even those with low rates of primary production. However, animals vary in their degree of dependence on these subsidies. We examined dietary sources for aquatic animals restricted to refugial habitats (waterholes) during the dry season in Australia’s wet–dry tropics, and show that allochthony is strongly size dependent. While small-bodied fishes and invertebrates derived a large proportion of their diet from autochthonous sources within the waterhole (phytoplankton, periphyton, or macrophytes), larger animals, including predatory fishes and crocodiles, demonstrated allochthony from seasonally inundated floodplains, coastal zones or the surrounding savanna. Autochthony declined roughly 10% for each order of magnitude increase in body size. The largest animals in the food web, estuarine crocodiles (Crocodylus porosus), derived ~80% of their diet from allochthonous sources. Allochthony enables crocodiles and large predatory fish to achieve high biomass, countering empirically derived expectations for negative density vs. body size relationships. These results highlight the strong degree of connectivity that exists between rivers and their floodplains in systems largely unaffected by river regulation or dams and levees, and how large iconic predators could be disproportionately affected by these human activities.     

QTL mapping for two commercial traits in farmed saltwater crocodiles (Crocodylus porosus)

The recent generation of a genetic linkage map for the saltwater crocodile (Crocodylus porosus) has now made it possible to carry out the systematic searches necessary for the identification of quantitative trait loci (QTL) affecting traits of economic, as well as evolutionary, importance in crocodilians. In this study, we conducted genome‐wide scans for two commercially important traits, inventory head length (which is highly correlated with growth rate) and number of scale rows (SR, a skin quality trait), for the existence of QTL in a commercial population of saltwater crocodiles at Darwin Crocodile Farm, Northern Territory, Australia. To account for the uncommonly large difference in sex‐specific recombination rates apparent in the saltwater crocodile, a duel mapping strategy was employed. This strategy employed a sib‐pair analysis to take advantage of our full‐sib pedigree structure, together with a half‐sib analysis to account for, and take advantage of, the large difference in sex‐specific recombination frequencies. Using these approaches, two putative QTL regions were identified for SR on linkage group 1 (LG1) at 36 cM, and on LG12 at 0 cM. The QTL identified in this investigation represent the first for a crocodilian and indeed for any non‐avian member of the Class Reptilia. Mapping of QTL is an important first step towards the identification of genes and causal mutations for commercially important traits and the development of selection tools for implementation in crocodile breeding programmes for the industry.     

MHC class I of saltwater crocodiles (Crocodylus porosus): polymorphism and balancing selection

Saltwater crocodiles are in high demand for the production of luxury fashion items. However, their susceptibility to disease incurs substantial losses and it is hoped to be able to genetically select these animals for disease resistance. So far, this has only been enabled by phenotypic selection. Investigating the major histocompatibility complex (MHC) could provide insight into the ability of an individual to respond to pathogens acting as a selective pressure on the host. Here, we assessed genetic diversity and a role of selection in shaping the diversity of MHC class I exon 3 among 42 saltwater crocodiles from nine river basins in the Northern Territory, Australia. We generated 640 sequences using cloning and sequencing methods and identified 43 MHC variants among them. Phylogenetic analyses clustered these variants into two major clades, which may suggest two gene lineages. We found the number of variants within an individual varying between one and seven, indicating that there are at least four gene loci in this species. Selection detection analyses revealed an elevated ratio of nonsynonymous to synonymous substitutions (mean?=?1.152 per codon), suggesting balancing selection. Population differentiation analyses revealed that the MHC did not show structuring among the river basins, and there were some shared variants among them. This may be a result of possible gene flow and/or similar selection pressures among populations. These findings provide background knowledge to identify potential MHC markers, which could be used for selecting genetically variable individuals for future disease associations. All MHC class I exon 3 sequences reported in this paper were submitted to the GenBank database with following accession numbers: HQ008785–HQ008789, HQ008791–HQ008798, HQ008808–HQ008815, HQ008824, HQ008826–HQ008830, HQ008835, HQ008839, HQ008842–HQ008850, and JX023536–JX023540.     

Isolation of Sindbis (alphavirus) and Leanyer viruses from mosquitoes collected in the Northern Territory of Australia, 1974.

Mosquitoes collected near Darwin, Northern Territory, in 1974 yielded two virus strains. One was identified as Sindbis virus, not previously isolated from the Northern Territory. The other is antigenically distinct from viruses previously isolated from arthropods in Australia, and the name "Leanyer" is proposed for it. Its properties suggest that it may be a togavirus serologically unrelated to available alphaviruses and flaviviruses.     

Molecular assessment of the genetic integrity,distinctiveness and phylogeographic context of the Saltwater crocodile (<Emphasis Type="Italic">Crocodylus porosus</Emphasis>) on Palau

The saltwater crocodile (Crocodylus porosus) is the largest and most broadly distributed crocodilian species, and thus is of special conservation and economic interest. Similar to other parts of its range throughout the Indo-Pacific, C. porosus distributed in the Republic of Palau have experienced a severe population decline over the past century primarily due to commercial hunting and eradication campaigns. In addition, several thousand crocodiles of undocumented species and origin were imported into Palau during the 1930’s for commercial farming purposes, potentially polluting the gene pool of the endemic saltwater crocodiles. Analysis of 39 individuals collected throughout the Republic of Palau revealed a single mitochondrial DNA control region haplotype shared by populations sampled in Sulawesi, Borneo and Australia. The mtDNA results, in combination with microsatellite genotypic data at six loci, detected no evidence for inter-specific hybridization between endemic Palauan C. porosus and potentially introduced Crocodylus species. There was no evidence for a genetic bottleneck in the Palauan population, however an excess of rare alleles was identified, indirectly suggesting a recent history of admixture potentially linked to introductions of non-native C. porosus. Following from these findings, Palauan C. porosus should be included in the single ESU previously established for all saltwater crocodiles given the recovery of a fixed, but geographically widespread haplotype. Although Palauan C. porosus exhibited significant genetic differentiation relative to all other sampled populations, it’s delineation as a distinct management unit is precluded at the present time by evidence that the genetic integrity of the population may have been compromised by the introduction of non-native saltwater crocodiles.     

Some observations on the breeding, age structure, dispersion and habitat of populations of Macropus robustus and Macropus antilopinus (Marsupialia)

Differences in breeding, population structure, dispersion and habitat are described between various species and subspecies of wallaroo (Macropus robustus robustus; M. r. cervinus; M. r. alligatoris; M. r. erubescens; Macropus antilopinus; Macropus bernardus).
Pouch young of Macropus robustus erubescens in western New South Wales were born throughout the year, while in both M. r. alligatoris and M. antilopinus then Northern Territory, most pouch young found were born during March and April.
In the populations of wallaroos in western New South Wales and the Northern Territory where there had been no systematic shooting of wallaroos for many years, 11|X% of the animals were immature. In the New England district of New South Wales where regular shooting occurs, 46|X% of the animals were immature.
The habitat of M. r. alligatoris of the Northern Territory was very similar to that of M. erubescens in inland Australia, amongst rocky hills and gullies. M. antilopinus , which is sympatric with M. r. alligatoris in the Northern Territory, also occurred in the rocky hills, but it was also found in open savannah woodland in flat and gently undulating country.
M. r. erubescens and M. r. alligatoris were almost always seen alone or in pairs, while M. antilopinus often formed larger groups.     

Isolation and characterisation of a novel Bohle-like virus from two frog species in the Darwin rural area, Australia

Twelve captive magnificent tree frogs Litoria splendida and 2 green tree frogs L. caerulea on a property in the Darwin rural area (Northern Territory, Australia) either died or were euthanased after becoming lethargic or developing skin lesions. Samples from both species of frog were submitted for histopathology and virus isolation. An irido-like virus was cultured from tissue samples taken from both species and was characterised using electron microscopy, restriction enzyme digests and nucleic acid amplification and sequencing. The isolates were determined to belong to the genus Ranavirus, were indistinguishable from each other and shared a 98.62% nucleotide similarity and a 97.32% deduced amino acid homology with the Bohle iridovirus over a 1161 bp region of the major capsid gene. This is the first isolation of a ranavirus from amphibians in the Northern Territory and the first report of natural infection in these 2 species of native frog. The virus is tentatively named Mahaffey Road virus (MHRV).     

Genetic structure of introduced swamp buffalo subpopulations in tropical Australia

High densities of introduced herbivores can damage sensitive ecosystems, increase the risk of extinction of native biota, and host and spread disease. An essential step in managing large ‘feral’ animal populations is to quantify how they use habitats so that management interventions, such as culling, can be targeted to reduce densities and to minimize migration into areas from which animals have been removed. An effective method to quantify animal movements is by measuring landscape‐scale genetic population structure. We describe the genetic population structure of one of Australia's more destructive introduced mammals – the Asian swamp buffalo (Bubalus bubalis). We collected 524 skin samples from buffalo across their range in the Northern Territory of Australia. Allelic diversity in the Northern Territory population was low compared to those reported from populations in their native Asian habitats. The Australian population is tentatively made of three subpopulations; Melville Island, Eastern Arnhem and Central‐Western Arnhem populations. The Melville Island population is represented by a single cluster, while the Eastern Arnhem population has three clusters and the Central‐Western Arnhem population seven clusters. We found some support for isolation by distance across all the sampled populations, but little evidence for this relationship when comparing the two well‐mixed mainland meta‐populations. Despite their small founder populations and limited genetic variation, the persistence of buffalo in Australia has likely been aided by release from high predation, parasitism and disease typical of their native habitats.     

Conservation genomics in the fight to help the recovery of the critically endangered Siamese crocodile Crocodylus siamensis

Endangered species are often characterized by low genetic diversity and it is imperative for conservation efforts to incorporate the knowledge obtained from genetic studies for effective management. However, despite the promise of technological advances in sequencing, application of genome‐wide data to endangered populations remains uncommon. In the present study we pursued a holistic conservation‐genomic approach to inform a field‐based management programme of a Critically Endangered species, the Siamese crocodile Crocodylus siamensis. Using thousands of single nucleotide polymorphisms from throughout the genome, we revealed signals of introgression from two other crocodile species within our sample of both wild and captive‐bred Siamese crocodiles from Cambodia. Our genetic screening of the Siamese crocodiles resulted in the subsequent re‐introduction of 12 individuals into the wild as well as the selection of four individuals for captive breeding programmes. Comparison of intraspecific genetic diversity revealed an alarmingly low contemporary effective population size in the wild (<50) with evidence of a recent bottleneck around Tonle Sap Lake. We also projected a probable future extinction in the wild (within fewer than five generations) in this population in the absence of re‐introduction efforts. However, an increase in the number of potential breeders through re‐introductions, including the one resulting from this project, could counter this trend. Our results have been implemented in ongoing re‐introduction and captive breeding programmes, with major implications for the conservation management of Siamese crocodiles, and provide a blueprint for the rescue effort of other “terminally ill” populations of critically endangered species.     

New species and new record of Tetranychus Dufour from Australia, with a key to the major groups in this genus based on females (Acari: Prostigmata: Tetranychidae)

A new species of spider mite, Tetranychus bunda sp. n., is described and illustrated from Australia. It was found damaging the foliage of Desmodium tortuosum (Sw.) DC. (Fabaceae) in Darwin, Northern Territory. In addition, the geographical range of Tetranychus fijiensis Hirst is extended to include Australia. This species was found in the Northern Territory feeding on frangipani ( Plumeria sp., Apocynaceae), betel palm ( Areca catechu L., Arecaceae) and Macarthur feather palm ( Ptychosperma macarthurii [H. Wendl. ex Veitch] (H. Wendl. ex Hook. f., Arecaceae)). Details of the biology of T. bunda sp. n. and T. fijiensis are given. A key to the major groups of Tetranychus Dufour of the world, based on females, is presented and species known to occur in Australia are outlined.     

Potential effects of El Niño-South Oscillation (ENSO) on growth of the American crocodile, Crocodylus acutus (Crocodylia: Crocodilydae) in captivity

Temperature affects growth rate of crocodiles. However, no information exists about the effects of temperature by El Niño-South Oscillation (ENSO) on crocodiles. In this paper, we present information about the effect of ENSO on total length and body mass of Crocodylus acutus in captivity during 1997–2001. We did not observe differences in total length among years, but we did so in body mass. Furthermore, we observed that warm episodes of ENSO were associated with a higher average total length and cold episodes represented a higher average of body mass. Sea surface temperature (SST) was significantly related with total length; however, the relationship between SST and body mass was unclear. We suggest that ENSO effects on growth rates of crocodiles need to be considered as an important factor on the management of captive populations.     

Phylogeography of the antilopine wallaroo (Macropus antilopinus) across tropical northern Australia

The distribution of antilopine wallaroo, Macropus antilopinus, is marked by a break in the species’ range between Queensland and the Northern Territory, coinciding with the Carpentarian barrier. Previous work on M. antilopinus revealed limited genetic differentiation between the Northern Territory and Queensland M. antilopinus populations across this barrier. The study also identified a number of divergent lineages in the Northern Territory, but was unable to elucidate any geographic structure. Here, we re‐examine these results to (1) determine phylogeographic patterns across the range of M. antilopinus and (2) infer the biogeographic barriers associated with these patterns. The tropical savannahs of northern Australia: from the Cape York Peninsula in the east, to the Kimberley in the west. We examined phylogeographic patterns in M. antilopinus using a larger number of samples and three mtDNA genes: NADH dehydrogenase subunit 2, cytochrome b, and the control region. Two datasets were generated and analyzed: (1) a subset of samples with all three mtDNA regions concatenated together and (2) all samples for just control region sequences that included samples from the previous study. Analysis included generating phylogenetic trees based on Bayesian analysis and intraspecific median‐joining networks. The contemporary spatial structure of M. antilopinus mtDNA lineages revealed five shallow clades and a sixth, divergent lineage. The genetic differences that we found between Queensland and Northern Territory M. antilopinus samples confirmed the split in the geographic distribution of the species. We also found weak genetic differentiation between Northern Territory samples and those from the Kimberley region of Western Australia, possibly due to the Kimberley Plateau–Arnhem Land barrier. Within the Northern Territory, two clades appear to be parapatric in the west, while another two clades are broadly sympatric across the Northern Territory. MtDNA diversity of M. antilopinus revealed an unexpectedly complex evolutionary history involving multiple sympatric and parapatric mtDNA clades across northern Australia. These phylogeographic patterns highlight the importance of investigating genetic variation across distributions of species and integrating this information into biodiversity conservation.     

Rainfall,groundwater and refuges: Predicting extinctions of Australian tropical mammal species

Abstract A general decline in populations of some savanna mammal species has occurred since the mid-1980s in a fairly pristine national park environment in the Australian wet-dry tropics. Terrestrial native rodents have exhibited the greatest decline and marsupials the least. During the same period, waterholes have dried up and the previous strong association of mammals with riparian vegetation has diminished. A regional index of the level of groundwater was developed from 16 unexploited bores from across the northern half of the Northern Territory. Predicted mean groundwater values over 28 years showed a strong increase throughout the 1970s and a similar decrease throughout the 1980s. Using data since 1986, strong correlations between mammal numbers and groundwater levels for the preceding two years, and much weaker relationships with rainfall, were obtained. In turn, the groundwater levels were best correlated with an eight-year running mean of rainfall for both Darwin and Alice Springs and an eleven-year running mean for the Southern Oscillation Index. Extrapolating backward in time, cumulative pressure variation at Darwin showed two extended periods of predicted low ground-water values, 1900s–1920s and 1940s. Both periods were preceded by the last records of a number of now-extinct mammals from central Australia. A third trough in the early 1960s suggests another period of extinction in central Australia, previously unappreciated due to the lack of survey work in the 1950s. Further, by this analysis, the past 20 years has been the best period for mammals since weather records commenced. Analysis of continental-scale distributions of mammals showed evidence of fluctuations suggesting rocky areas are important refuges for some species during periods of low groundwater levels. In contrast to those in savanna habitats, the mammals of the extensive wetland areas fluctuated in harmony with rainfall on a short-term basis except where habitat is flooded. It is the species which occur only in savanna but not also in rocky or wetland habitats which are most at risk. A number of other species-vulnerability characteristics were identified: riparian vegetation specificity; the degree to which they fall within the critical size range (35 g-5. 5 kg); degree of semelparity; smallness of population size; and smallness of geographic range. Those savanna species with annual life histories strongly associated with riparian areas are likely to be in greatest jeopardy. The species which appear to be most vulnerable in northwestern Australia are Conilurus penicillatus, Mesembriomys gouldii, Mesembriomys macrurus, Antechinus bellus, Phascogale tapoatafa and Rattus tunneyi. Our recent benign climatic history has coincided with the great public environmental awakening and upsurge in environmental research and management efforts. This historical accident has probably led us to overstate the negative effects of human impact and also our ability to change the course of biological history by ameliorating human impact. Our distorted view of these factors has further led us to over-emphasize research of a spatial nature to the detriment of temporal studies. We must redress this balance.     

Phylogenetic group distribution among <Emphasis Type="Italic">Escherichia coli</Emphasis> isolated from rivers in São Paulo State,Brazil

The phylogenetic group distribution of Escherichia coli strains isolated from the Sorocaba and Jaguari Rivers located in the State of São Paulo, Brazil, is described. E. coli strains from group D were found in both rivers while one strain from group B2 was isolated from the Sorocaba river. These two groups often include strains that can cause extraintestinal diseases. Most of the strains analyzed were allocated into the phylogenetic groups A and B1, supporting the hypothesis that strains from these phylogenetic groups are more abundant in tropical areas. Though both rivers are located in urbanized and industrialized areas where the main source of water pollution is considered to derive from domestic sewage, our results suggest that the major sources of contamination in the sampling sites of both rivers might have originated from animals and not humans.     

Failure of a stocking policy, of hatchery reared brown trout, Salmo trutta L., in Asturias, Spain, detected using LDH-5* as a genetic marker

A useful genetic marker exists through the apparent fixation of the LDH-5 * 100 allele in wild populations of brown trout in rivers from Asturias, Spain, contrasted with the near fixation of the LDH-5 * 90 allele in hatchery populations used to stock these rivers. In sampling locations where natural reproduction occurred, the * 100 allele was found exclusively in all areas having no record of hatchery stocking. The * 100 allele also predominated in three stocked areas having natural reproduction; in two of these areas a few individuals of the 0 + age class were homozygous for the * 90 allele. These data indicated that all catchable and reproductive fish originated from indigenous populations and thus the policy of hatchery supplementation was a failure in these areas.     

Restoration Potential of Bighorn Sheep in a Prairie Region

Efforts to recover Rocky Mountain bighorn sheep (Ovis canadensis canadensis) throughout western North America have had limited success with the majority of current populations remaining in small and isolated areas on a fraction of their historical range. Prairie environments with rugged topography throughout the Northern Great Plains ecoregion were historically occupied by relatively robust bighorn sheep populations. We predicted there is likely unrealized potential habitat for restoring bighorn sheep to these areas; however, relatively little attention has been devoted to identifying habitat in unoccupied prairie regions. We used global positioning system (GPS)-collar data collected from 43 female bighorn sheep in 2 populations located in the eastern Montana, USA, portion of the Northern Great Plains during 2014–2018 to estimate a population-level annual resource selection model and identify the important factors affecting bighorn sheep resource selection. We extrapolated model predictions across eastern Montana's prairie region and identified potential habitat to understand restoration potential and assist with future translocations of bighorn sheep. Resource selection of bighorn sheep was most strongly associated with terrain slope and ruggedness, tree canopy cover, and a normalized difference vegetation index metric. Within currently unoccupied areas of the historical range, the model extrapolation predicted 7,211 km² of habitat, with most owned and managed by private landowners (44%), Bureau of Land Management (33%), and the United States Fish and Wildlife Service (15%). Our results provide an empirical evaluation of landscape covariates influencing resource selection of bighorn sheep occupying prairie environments and provide a habitat model that may be generalizable to other areas in the Northern Great Plains ecoregion. We demonstrate substantial potential for restoration opportunities of bighorn sheep in the Northern Great Plains ecoregion. Broad restoration of bighorn sheep across the ecoregion would likely require strong collaboration among and between public resource managers, private landowners, and livestock producers given the heterogeneous land ownership patterns, management strategies, and domestic sheep distributions. © 2020 The Wildlife Society.     

Recruitment variability of resident brown trout in peripheral populations from southern Europe

1. Population regulation was studied for seven consecutive years (1992–98) in five rivers at the periphery of the distribution of Salmo trutta, where the fish were living under environmental constraints quite different from those of the main distribution area. 2. Recruitment is naturally highly variable and the populations had been earlier classified as overexploited. Thus we expected that densities of young trout in most populations would be too low for density‐dependent mortality to operate. We tested this by fitting the abundance of recruits to egg densities over seven consecutive years (stock–recruitment relationship), and used the results to judge whether exploitation should be restricted in the interests of conserving the populations. 3. The density of 0+ trout in early September, as well as the initial density of eggs and parents, varied greatly among localities and years. The data for all populations fitted the Ricker stock–recruitment model. The proportion of variance explained by the population curves varied between 32% and 51%. However, in most cases the observations were in the density‐independent part of the stock–recruitment curve, where densities of the recruits increased proportionally with egg densities. 4. Our findings suggest that recruitment densities in most rivers and years were below the carrying capacity of the habitats. Although density‐dependent mechanisms seemed to regulate fish abundance in some cases, environmental factors and harvesting appeared generally to preclude populations from reaching densities high enough for negative feedbacks to operate. The findings thus lend support to Haldane’s (1956) second hypothesis that changes in population density are primarily due to density‐independent factors in unfavourable areas and areas with low density due to exploitation. Exploitation should be reduced to allow natural selection to operate more effectively.     

Fungal endophytes of native Gossypium species in Australia

Fungal endophytes of 17 genera were found in stems of four native Gossypium species (G. australe, G. bickii, G. nelsonii, G. sturtianum) collected from inland areas in Queensland, the Northern Territory, and South Australia in 2001. Phoma, Alternaria, Fusarium, Botryosphaeria, Dichomera, and Phomopsis were common, accounting for 58, 18, 11, 3, 1, and 1 % of the 281 recovered isolates, respectively, and occurring in 47, 29, 19, 5, 5, and 4 % of the 79 sampled populations. Among the four Gossypium species in Queensland and the Northern Territory, Alternaria spp. and Fusarium spp. had the greatest recovery frequency in G. bickii stems. The recovery frequencies of Phoma spp. and Alternaria spp. were significantly greater in the G. sturtianum stems collected from South Australia than in those from Queensland and the Northern Territory. Pathogenicity of 42 representative isolates was tested on cultivated cotton (G. hirsutum). All isolates caused some localized discoloration in stem tissue when inoculation was conducted with the stem puncturing method, but none of the isolates could induce any foliar symptoms during the five-week experimental period by either inoculation method (root dipping or stem puncturing), suggesting that the endophytic fungi of native Gossypium species are unlikely sources of cotton pathogens.