77 results on '"Humphreys WF"'
Search Results
2. Consequences of evolutionary transitions in changing photic environments
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Tierney, SM, Friedrich, M, Humphreys, WF, Jones, TM, Warrant, EJ, Wcislo, WT, Tierney, SM, Friedrich, M, Humphreys, WF, Jones, TM, Warrant, EJ, and Wcislo, WT
- Abstract
Light represents one of the most reliable environmental cues in the biological world. In this review we focus on the evolutionary consequences to changes in organismal photic environments, with a specific focus on the class Insecta. Particular emphasis is placed on transitional forms that can be used to track the evolution from (1) diurnal to nocturnal (dim‐light) or (2) surface to subterranean (aphotic) environments, as well as (3) the ecological encroachment of anthropomorphic light on nocturnal habitats (artificial light at night). We explore the influence of the light environment in an integrated manner, highlighting the connections between phenotypic adaptations (behaviour, morphology, neurology and endocrinology), molecular genetics and their combined influence on organismal fitness. We begin by outlining the current knowledge of insect photic niches and the organismal adaptations and molecular modifications that have evolved for life in those environments. We then outline concepts and guidelines for future research in the fields of natural history, ethology, neurology, morphology and particularly the advantages that high throughput sequencing provides to these aspects of investigation. Finally, we highlight that the power of such integrative science lies in its ability to make phylogenetically robust comparative assessments of evolution, ones that are grounded by empirical evidence derived from a concrete understanding of organismal natural history.
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- 2017
3. Groundwater-dependent ecosystems and the dangers of groundwater overdraft: A review and an Australian perspective
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Nevill, TC, Hancock, PJ, Murray, BR, Ponder, WF, Humphreys, WF, Phillips, ML, Groom, PK, Nevill, TC, Hancock, PJ, Murray, BR, Ponder, WF, Humphreys, WF, Phillips, ML, and Groom, PK
- Abstract
In many parts of the world, access to groundwater is needed for domestic, agricultural and industrial uses, and global groundwater exploitation continues to increase. The significance of groundwater in maintaining the health of rivers, streams, wetlands and associated vegetation is often underestimated or ignored, resulting in a lack of scrutiny of groundwater policy and management. It is essential that management of groundwater resources considers the needs of natural ecosystems, including subterranean. We review the limited Australian literature on the ecological impacts of groundwater overdraft and place Australian information within an international context, focusing on lentic, lotie, stygobitic and hyporheic communities as well as riparian and phreatophytic vegetation, and some coastal marine ecosystems. Groundwater overdraft, defined as abstracting groundwater at a rate which prejudices ecosystem or anthropocentric values, can substantially impact natural communities which depend, exclusively or seasonally, on groundwater. Overdraft damage is often underestimated, is sometimes irreversible, and may occur over time scales at variance to those used by water management agencies in modelling, planning and regulation. Given the dangers of groundwater overdraft, we discuss policy implications in the light of the precautionary principle, and make recommendations aimed at promoting the conservation of groundwater-dependent ecosystems within a sustainable use context.
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- 2010
4. Stratification of the microbial community inhabiting an anchialine sinkhole
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Seymour, JR, Humphreys, WF, Mitchell, JG, Seymour, JR, Humphreys, WF, and Mitchell, JG
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Bundera Sinkhole in northwestern Australia is an anchialine ecosystem characterised by a highly stratified water column comprising a complex polymodal profile of several physico-chemical parameters. We studied the microscale and finescale dynamics of the resident microbial community within the sinkhole. Sub-millimetre scale distributions of phytoplankton abundance were measured in the top 8 m of the water column using a free-falling high resolution fluorometer. Depth profiles were characterised by a strong, 10 to 20 cm layer of elevated fluorescence, occurring at approximately 1 m depth, which despite changes in magnitude and width was found to persist during a 24 h sampling period. Near surface distributions of microbial populations were measured using a syringe sampling profiler, which allowed for collection of water samples at 5 cm resolution, and flow cytometric analysis. These samples revealed a complex microbial assemblage, with multiple subpopulations of viruses, bacteria and picophytoplankton present throughout the water column. Within 3 m profiles, the bacterial and virus populations showed marked shifts in relative abundance, with changes of over 35-fold observed across as little as 20 cm. Samples collected from the surface to a depth of 30 m by divers also revealed distinct peaks and layers in the relative abundance of the different bacteria and virus sub-populations, which often corresponded to heterogeneities in chemical and nutrient parameters, and at some depths indicated the prevalence of chemolithotrophic populations. The complex patterns described here represent the first comprehensive observations of microbial spatiotemporal dynamics throughout an anchialine ecosystem and reveal a highly structured microbial habitat consisting of discrete niches, each dominated by heterotrophic, phototrophic or chemoautotrophic microorganisms. © Inter-Research 2007.
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- 2007
5. Stratification of the microbial community inhabiting an anchialine sinkhole
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Seymour, JR, primary, Humphreys, WF, additional, and Mitchell, JG, additional
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- 2007
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6. Lasionectes exleyi, sp, nov., the first remipede crustacean recorded from Australia and the Indian Ocean, with a key to the world species
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Yager, J, primary and Humphreys, WF, additional
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- 1996
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7. Haptolana pholeta, sp. nov., The first subterranean flabelliferan isopod crustacean (Cirolanidae) from Australia
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Bruce, NL, primary and Humphreys, WF, additional
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- 1993
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8. Troglobitic millipedes (Diplopoda : Paradoxosomatidae) from semi-arid Cape Range, Western Australia: Systematics and biology
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Humphreys, WF, primary and Shear, WA, additional
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- 1993
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9. First record of Thermosbaenacea (Crustacea) from the Southern Hemisphere: a new species from a cave in tropical Western Australia
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Poore, GCB, primary and Humphreys, WF, additional
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- 1992
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10. Lasionectes exleyi, sp, nov., the first remipede crustacean recorded from Australia and the Indian Ocean, with a key to the world species
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Yager, J and Humphreys, WF
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The first remipede crustacean from the Southern Hemisphere and the Indian Ocean is reported. Lasionectes exleyi, sp. nov., is described from an anchialine cave on the Cape Range peninsula of Western Australia. This is the eleventh species of modern remipede to be described and the second species to be described in the genus Lasionectes. A key to all known species is presented. The discovery of remipedes in Australia represents the first occurrence of a genus other than Speleonectes off the Bahamas Banks and only the second continental occurrence of extant remipedes. The species is known from below a density interface in a single nutrient-enriched cave.
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- 1996
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11. Small Mammal Populations in Pine and Native Forests in North-Eastern New South Wales.
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Barnett, JL, How, RA, and Humphreys, WF
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Populations of small mammals were examined in a 6 yr Pinus taeda plantation (extended to include similar age P. radiata) and adjacent native rain forest in north-east New South Wales, Australia. Of the 6 species trapped, Rattus fuscipes was the only one with viable populations in both vegetation types. R. lutreolus, R. rattus and Mus musculus were restricted to the plantation; Melomys cervinipes and Antechinus stuartii (except for a few individuals) were confined to the native forest.
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- 1977
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12. The Biology of the Northern Brown Bandicoot, Isoodon-Macrourus (Marsupialia, Peramelidae) at Mitchell Plateau, Western-Australia
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Kemper, C, Kitchener, DJ, Humphreys, WF, How, RA, Schmitt, LH, and Bradley, A
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Breeding, population dynamics and seasonal changes in physical and physiological parameters were examined in Isoodon macrourus at the Mitchell Plateau between September 1981 and November 1982. Females gave birth to litters of 2.5 1.0 (16) young between September and April. They produced up to three litters in a breeding season with an average interval between successive litters of 89.5 (51-108) days. Adult testosterone levels and scrota1 size began to increase in July and peaked in September 1982. The overall ratio of adult males to adult females was 1:0.54; it was 1:0.80 for pouch young. Females were more frequently trapped on sequential trips than were males. Density on the grids increased towards the end of the dry season (July and September 1982)-mostly as a result of increased numbers of females. Adult males and females moving onto the grids during the dry season tended to select different habitats. Adult males moved significantly more in the wet season (September 1981, January and April) than they did in the dry season (July and September 1982); they also moved significantly more than adult females in the wet season. Seasonal variations were recorded for most physical and physiological parameters. During the wet period from September 1981 to January 1982, body weight, haemoglobin, haematocrit and total plasma albumin declined, while total white blood cells and proportion of lymphocytes to granular leucocytes rose. This indicated that this period was one of change in condition for this species. Compared to adult females, adult males were larger and heavier, had higher values of haematocrit and lymphocytes, and lower values of granular leucocytes, free steroids, CBGBd and albumin bound corticosteroid. There was considerable between-year variability in condition of individuals and both sexes differed significantly in September 1981 and 1982 in their weight, haematocrit, total white blood cells, granular leucocytes, MCBC and testosterone. Individuals at disparate localities at the Mitchell Plateau showed similar seasonal physiological and physical responses, except for one grid where they were heavier.
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- 1989
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13. Haptolana pholeta, sp. nov., The first subterranean flabelliferan isopod crustacean (Cirolanidae) from Australia
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Bruce, NL and Humphreys, WF
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The genus Haptolana Bowman, 1966 is rediagnosed, and is characterised by the unique synapomorphy of pereopods 2–7 having an expanded propodus, the palm of which contains a V-shaped series of spines and a haptorial dactylus which folds in between these spines. Haptolana pholeta, from anchialine waters on Barrow Island, Western Australia, is described, and is distinguished from the two other species of Haptolana in possessing a frontal lamina that is anteriorly rounded, that separates the antennule bases and is visible in dorsal view.
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- 1993
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14. Troglobitic millipedes (Diplopoda : Paradoxosomatidae) from semi-arid Cape Range, Western Australia: Systematics and biology
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Humphreys, WF and Shear, WA
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Paradoxosomatid millipedes are an important component of the rich troglobitic fauna of the semi-arid tropical Cape Range, Western Australia. They are found in at least 55 of the 282 caves known from Cape Range covering >500 km⊃;. The millipedes occur in dense populations only in areas of high relative humidity and organic carbon content. They appear to be opportunistic and are able to grow and breed rapidly on the intermittently available patches of organic matter washed into the caves by unpredictable rainfall. A new genus of paradoxosomatid millipedes (Stygiochiropus, gen. nov.), comprising three species (S. communis, sp. nov., S. sympatricus, sp. nov., and S. isolatus, sp. nov.) is described from the caves. A key is provided for males, but females cannot be identified. The only widespread species (S. communis) separates into three provinces between which there are many fixed allelic differences, as determined by allozyme electrophoresis. Although these genetic provinces are separated by deep gorges that cut through the cavernous limestone into the underlying non-cavernous strata, the millipede populations cannot be separated using morphological criteria. The affinities of the millipedes are unknown, but they are part of a rich community of troglobites (>26 species) of which many species have affinities with the northern wet tropical forest fauna, rather than with the current semi-arid fauna.
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- 1993
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15. First record of Thermosbaenacea (Crustacea) from the Southern Hemisphere: a new species from a cave in tropical Western Australia
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Poore, GCB and Humphreys, WF
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The crustacean order Thermosbaenacea is reported for the first time from the Southern Hemisphere, from almost fresh water in a cave habitat in tropical Western Australia. Halosbaena tulki, sp. nov. belongs to a genus previously known only from saline waters in the West Indies, Columbia and Canary Is. The discovery is consistent with a very ancient origin of the order and distribution of the genus by plate movements following the breakup of Pangaea.
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- 1992
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16. Small Mammals of the Mitchell Plateau Region, Kimberley, Western-Australia
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Bradley, AJ, Kemper, CM, Kitchener, DJ, Humphreys, WF, and How, RA
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This paper presents the background for a series on the biology of small mammals in the Mitchell Plateau region, an area characterised by a wet-dry tropical climate. From June 1981 to December 1982, 19 species of small terrestrial mammals were captured at Mitchell Plateau. Of 17 species captured on eight mark-release grids, 13 clustered into four significant groups which reflected the major habitats of the region: (1) Sminthopsis virginiae, Leggadina sp. and Pseudomys nanus in riparian and plateau escarpment sites; (2) Phascogale tapoatafa, Trichosurus arnhemensis and Pseudomys laborifex in plateau open forest; (3) Conilurus penicillatus and Mesembriomys macrurus in open woodland and coastal mosaics; (4) the commoner species Dasyurus hallucatus, Isoodon macrourus, Melomys sp. cf. burtoni, Zyzomys argurus and S. woodwardi in an array of habitats. Rattus tunneyi, Pseudantechinus sp., Wyulda squamicaudata and Planigale maculata did not cluster significantly with other species. Two species, Pseudomys delicatulus and Mesembriomys gouldii, were represented by single specimens captured outside the capture-mark-release grids, in sandstone and plateau woodland respectively. Open forests, particularly on the lateritic plateau surfaces, had the richest and most diverse mammal assemblage over the entire study period. The vine thickets and sandstone contained relatively stable populations of fewer species, and several habitats had seasonally variable populations and species.
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- 1987
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17. Habitat Effects on Organ Weights, Longevity and Reproduction in the Mountain Brushtail Possum, Trichosurus caninus (Ogilby)
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Barnett, JL, How, R.A., and Humphreys, WF
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Fifty-seven mountain brushtail possums. Trichosurus caninus (Ogilby), were killed and examined from a population in north-eastern New South Wales; 34 were from preferred habitat and 23 from peripheral habitat. Maximum age attained was 17 y for females and 12 y for males. Body, kidney, spleen and male liver weights were greater (P<0.05) in peripheral habitat, and female adrenal glands were heavier (P< 0.05) in preferred habitat. The mean number of corpora lutea per year of reproductive life was greater in peripheral-habitat females (1.56 0.13 SE) than in preferred-habitat females (1.18 0.11; P<0.05). Adult sex ratio was parity in both habitats but themean annual sex ratio of pouch young was 2.5:1 male : female in preferred habitat and 0.7:1 in peripheral habitat. The phenotypic distri-bution of transferrin differed between habitats. The data suggest that T. caninus in preferred and peripheral habitats were sufficiently distinctive in morphological, demographic, behavioural and genetic characters to be considered distinct subpopulations.
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- 1982
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18. Effects of Habitat, Host Sex and Age on the Parasites of Trichosurus Caninus (Marsupialia: Phalangeridae) in North-Eastern New South Wales.
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Presidente, PJA, Barnett, JL, How, RA, and Humphreys, WF
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The condition of 57 Trichosurus caninus (Ogilby), and their ectoparasites, endoparasites and associated pathology were examined; ages and habitat status of these animals were known. Condition scores for females were greater (P<0.005) than those for males. Seven ectoparasite species (two ticks, five mites), two protozoan and seven helminth (one cestode, six nematodes) species were identified in T. caninus from both preferred and peripheral habitats. Prevalence of Amplicaecum robertsi (Sprent & Mines) larvae and the oxyurid nematode Adelonema trichosuri (Johnston & Mawson) were greater (P<0.05) in T. caninus from peripheral habitat than in preferred-habitat animals. Greater burdens (P<0.05) of the tick Ixodes holocyclus Neumann, two mites Trichosurolaelaps dixoa Domrow and 7. crassipes Womersley, and the trichostrongylid nematode Paraustrostrongylus trichosuri Mawson were found in peripheral-habitat T. caninus. Subadult males harboured greater Paraustrostrongylus burdens (P<0.05) than did subadult females or adult animals. Three Trichosurus vulpecula (Kerr) sympatric with peripheral-habitat T. caninus were also examined. One tick I. trichosuri Roberts, one mite T. crassipes and four helminth species: Bertiella trichosuri Khalil, A. robertsi, Paraustrostrongylus trichosuri and Parastrongyloides trichosuri Mackerras, were identified. The cestode B. trichosuri was recovered from the three T. vulpecula and four peripheral-habitat T. caninus, but only from one T. caninus from preferred habitat. Larval A. robertsi caused focal eosinophilic cholangiohepatitis with dilatation of affected bile ducts in livers of both Trichosurus spp. Eosinophilic vasculitis of hepatic portal veins was associated with ?Sprattia venacavincola (Spratt & Varughese) and focal granulomatous splenitis with sequestered microfilariae in T. caninus. Also, ?Marsupostrongylus minesi Spratt in dilated alveoli caused mild pulmonary inflammation. There were no pathological changes associated with intestinal tract parasites. Free corticosteroid levels in preferred-habitat female T. caninus were greater (P<0.05) than in those from peripheral habitat. This correlated with hyperplastic changes in adrenal glands of these females, but not with parasite burdens.
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- 1982
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19. Blood parameters in natural populations of Trichosurus species (Marsupialia : Phalangeridae) II. Influence of habitat and population strategies of T. caninus and T. vulpecula
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Barnett, JL, How, RA, and Humphreys, WF
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Body weight and six blood parameters were determined in T. caninus and T. vulpecula from their preferred and peripheral habitats. Habitat had a large effect on T. caninus. Of the seven parameters measured, six (body weight, red blood cell count, haemoglobin concentration, haematocrit and plasma protein and lipid concentrations) were higher in the population from the peripheral habitat than in that from the preferred habitat. Only body weight was different in T. vulpecula, being higher in the peripheral than in the preferred habitat population. There were differences between T. caninus and T. vulpecula in four of the measured parameters (body weight, haematocrit, haemoglobin concentration and red blood cell count) irrespective of habitat, whereas plasma lipid concentration was the same in T. caninus from peripheral habitat and T. vulpecula, but differed in T. caninus between habitats. Four parameters showed significant seasonal variation in preferred-habitat T. caninus, three in peripheral-habitat T. caninus and one in T. vulpecula. However, the pattern of seasonal change in peripheral-habitat T. caninus was more similar to that in T. vulpecula than to that in preferred-habitat T. caninus, suggesting a physiological shift in peripheral-habitat T. caninus towards that of the more r-selected T. vulpecula. No differences were found between resident and dispersing T. caninus. T. caninus which had lost a pouch young and failed to maintain another in the same year had lower haematocrit and plasma lipid concentration than females in other reproductive states. It is suggested that the measurement of physiological responsiveness of populations may aid the understanding of adaptive strategies.
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- 1979
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20. Blood Parameters in Natural Populations of Trichosurus Species (Marsupialia: Phalangeridae). I. Age, Sex and Seasonal Variation in T. Caninus and T. Vulpecula. Ii. Influence of Habitat and Population Strategies of T. Caninus and T. Vulpecula.
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Barnett, JL, How, RA, and Humphreys, WF
- Abstract
Age, sex and seasonal related changes in body weight and blood parameters were determined for T caninus and T. vulpecula, whose distribution overlapped in part of the study area. In T. caninus age-related changes occurred in body weight, mean plasma glucose and protein concentrations and haematocrit. Seasonal changes occurred in plasma glucose and protein concentrations, haemoglobin concentration and red blood cell count. There were sexual dimorphisms in haematocrit, haemoglobin concentration and red blood cell count in both species; the mean values were greater in males. T. vulpecula also exhibited a sexual dimorphism in body weight (males > females). The only seasonal change in T. vulpecula was in haemoglobin concentration. Comparison of the species as adults showed that T. caninus had higher mean levels of body weight, haematocrit and haemoglobin concentration, while plasma lipid concentration and red blood cell counts were greater in T vulpecula. These species differences may be a reflection of the diets of the two species. In addition the measured parameters showed greater seasonal variation in T. caninus, a K-selected species, than in T. vulpecula, which is more r-selected.
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- 1979
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21. Exploring virus-host-environment interactions in a chemotrophic-based underground estuary.
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Ghaly TM, Focardi A, Elbourne LDH, Sutcliffe B, Humphreys WF, Jaschke PR, Tetu SG, and Paulsen IT
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Background: Viruses play important roles in modulating microbial communities and influencing global biogeochemistry. There is now growing interest in characterising their ecological roles across diverse biomes. However, little is known about viral ecology in low-nutrient, chemotrophic-based environments. In such ecosystems, virus-driven manipulation of nutrient cycles might have profound impacts across trophic levels. In particular, anchialine environments, which are low-energy underground estuaries sustained by chemotrophic processes, represent ideal model systems to study novel virus-host-environment interactions., Results: Here, we employ metagenomic sequencing to investigate the viral community in Bundera Sinkhole, an anchialine ecosystem rich in endemic species supported by microbial chemosynthesis. We find that the viruses are highly novel, with less than 2% representing described viruses, and are hugely abundant, making up as much as 12% of microbial intracellular DNA. These highly abundant viruses largely infect important prokaryotic taxa that drive key metabolic processes in the sinkhole. Further, the abundance of viral auxiliary metabolic genes (AMGs) involved in nucleotide and protein synthesis was strongly correlated with declines in environmental phosphate and sulphate concentrations. These AMGs encoded key enzymes needed to produce sulphur-containing amino acids, and phosphorus metabolic enzymes involved in purine and pyrimidine nucleotide synthesis. We hypothesise that this correlation is either due to selection of these AMGs under low phosphate and sulphate concentrations, highlighting the dynamic interactions between viruses, their hosts, and the environment; or, that these AMGs are driving increased viral nucleotide and protein synthesis via manipulation of host phosphorus and sulphur metabolism, consequently driving nutrient depletion in the surrounding water., Conclusion: This study represents the first metagenomic investigation of viruses in anchialine ecosystems, and provides new hypotheses and insights into virus-host-environment interactions in such 'dark', low-energy environments. This is particularly important since anchialine ecosystems are characterised by diverse endemic species, both in their microbial and faunal assemblages, which are primarily supported by microbial chemosynthesis. Thus, virus-host-environment interactions could have profound effects cascading through all trophic levels., (© 2024. The Author(s).)
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- 2024
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22. Groundwater is a hidden global keystone ecosystem.
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Saccò M, Mammola S, Altermatt F, Alther R, Bolpagni R, Brancelj A, Brankovits D, Fišer C, Gerovasileiou V, Griebler C, Guareschi S, Hose GC, Korbel K, Lictevout E, Malard F, Martínez A, Niemiller ML, Robertson A, Tanalgo KC, Bichuette ME, Borko Š, Brad T, Campbell MA, Cardoso P, Celico F, Cooper SJB, Culver D, Di Lorenzo T, Galassi DMP, Guzik MT, Hartland A, Humphreys WF, Ferreira RL, Lunghi E, Nizzoli D, Perina G, Raghavan R, Richards Z, Reboleira ASPS, Rohde MM, Fernández DS, Schmidt SI, van der Heyde M, Weaver L, White NE, Zagmajster M, Hogg I, Ruhi A, Gagnon MM, Allentoft ME, and Reinecke R
- Subjects
- Biodiversity, Fresh Water, Environmental Pollution, Ecosystem, Groundwater
- Abstract
Groundwater is a vital ecosystem of the global water cycle, hosting unique biodiversity and providing essential services to societies. Despite being the largest unfrozen freshwater resource, in a period of depletion by extraction and pollution, groundwater environments have been repeatedly overlooked in global biodiversity conservation agendas. Disregarding the importance of groundwater as an ecosystem ignores its critical role in preserving surface biomes. To foster timely global conservation of groundwater, we propose elevating the concept of keystone species into the realm of ecosystems, claiming groundwater as a keystone ecosystem that influences the integrity of many dependent ecosystems. Our global analysis shows that over half of land surface areas (52.6%) has a medium-to-high interaction with groundwater, reaching up to 74.9% when deserts and high mountains are excluded. We postulate that the intrinsic transboundary features of groundwater are critical for shifting perspectives towards more holistic approaches in aquatic ecology and beyond. Furthermore, we propose eight key themes to develop a science-policy integrated groundwater conservation agenda. Given ecosystems above and below the ground intersect at many levels, considering groundwater as an essential component of planetary health is pivotal to reduce biodiversity loss and buffer against climate change., (© 2023 The Authors. Global Change Biology published by John Wiley & Sons Ltd.)
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- 2024
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23. Evolution of endoglucanase genes in subterranean and surface isopod crustaceans from Central Western Australia.
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Javidkar M, Cooper SJB, Shokri Bousjein N, Humphreys WF, King RA, and Austin AD
- Abstract
Recent studies have identified a significant number of endogenous cellulase genes in various arthropods, including isopods, allowing them to process hydrocarbons efficiently as a food source. While this research has provided insight into underlying gene-level processes in cellulose decomposition by arthropods, little is known about the existence and expression of cellulase genes in species from cave environments where carbohydrates are sparse. To investigate whether endogenous cellulase genes are maintained in subterranean species, we sequenced the transcriptomes of two subterranean paraplatyarthrid isopod species from calcrete (carbonate) aquifers of central Western Australia and a related surface isopod species. Seven protein-coding open-reading frames associated with endoglucanase genes were identified in all species. Orthology inference analyses, using a wide range of cellulase sequences from available databases, supported the endogenous origin of the putative endoglucanase genes. Selection analyses revealed that these genes are primarily subject to purifying selection in most of the sites for both surface and subterranean isopod species, indicating that they are likely to encode functional peptides. Furthermore, evolutionary branch models supported the hypothesis of an adaptive shift in selective pressure acting on the subterranean lineages compared with the ancestral lineage and surface species. Branch-site models also revealed a few amino acid sites on the subterranean branches to be under positive selection, suggesting the acquisition of novel adaptations to the subterranean environments. These findings also imply that hydrocarbons exist in subsurface aquifers, albeit at reduced levels, and have been utilized by subterranean isopods as a source of energy for millions of years., Competing Interests: The authors have no conflicts of interest to declare., (© 2023 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)
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- 2023
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24. Sensitivity of northwest Australian tropical cyclone activity to ITCZ migration since 500 CE.
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Denniston RF, Ummenhofer CC, Emanuel K, Ingrosso R, Pausata FSR, Wanamaker AD, Lachniet MS, Carr KT, Asmerom Y, Polyak VJ, Nott J, Zhang W, Villarini G, Cugley J, Brooks D, Woods D, and Humphreys WF
- Abstract
Tropical cyclones (TCs) regularly form in association with the intertropical convergence zone (ITCZ), and thus, its positioning has implications for global TC activity. While the poleward extent of the ITCZ has varied markedly over past centuries, the sensitivity with which TCs responded remains poorly understood from the proxy record, particularly in the Southern Hemisphere. Here, we present a high-resolution, composite stalagmite record of ITCZ migrations over tropical Australia for the past 1500 years. When integrated with a TC reconstruction from the Australian subtropics, this time series, along with downscaled climate model simulations, provides an unprecedented examination of the dependence of subtropical TC activity on meridional shifts in the ITCZ. TCs tracked the ITCZ at multidecadal to centennial scales, with a more southward position enhancing TC-derived rainfall in the subtropics. TCs may play an increasingly important role in Western Australia's moisture budgets as subtropical aridity increases due to anthropogenic warming.
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- 2023
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25. Differential transcriptomic responses to heat stress in surface and subterranean diving beetles.
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Beasley-Hall PG, Bertozzi T, Bradford TM, Foster CSP, Jones K, Tierney SM, Humphreys WF, Austin AD, and Cooper SJB
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- Animals, Ecosystem, Heat-Shock Response genetics, Transcriptome, Coleoptera genetics
- Abstract
Subterranean habitats are generally very stable environments, and as such evolutionary transitions of organisms from surface to subterranean lifestyles may cause considerable shifts in physiology, particularly with respect to thermal tolerance. In this study we compared responses to heat shock at the molecular level in a geographically widespread, surface-dwelling water beetle to a congeneric subterranean species restricted to a single aquifer (Dytiscidae: Hydroporinae). The obligate subterranean beetle Paroster macrosturtensis is known to have a lower thermal tolerance compared to surface lineages (CT
max 38 °C cf. 42-46 °C), but the genetic basis of this physiological difference has not been characterized. We experimentally manipulated the thermal environment of 24 individuals to demonstrate that both species can mount a heat shock response at high temperatures (35 °C), as determined by comparative transcriptomics. However, genes involved in these responses differ between species and a far greater number were differentially expressed in the surface taxon, suggesting it can mount a more robust heat shock response; these data may underpin its higher thermal tolerance compared to subterranean relatives. In contrast, the subterranean species examined not only differentially expressed fewer genes in response to increasing temperatures, but also in the presence of the experimental setup employed here alone. Our results suggest P. macrosturtensis may be comparatively poorly equipped to respond to both thermally induced stress and environmental disturbances more broadly. The molecular findings presented here have conservation implications for P. macrosturtensis and contribute to a growing narrative concerning weakened thermal tolerances in obligate subterranean organisms at the molecular level., (© 2022. The Author(s).)- Published
- 2022
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26. Parallel decay of vision genes in subterranean water beetles.
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Langille BL, Tierney SM, Bertozzi T, Beasley-Hall PG, Bradford TM, Fagan-Jeffries EP, Hyde J, Leijs R, Richardson M, Saint KM, Stringer DN, Villastrigo A, Humphreys WF, Austin AD, and Cooper SJB
- Subjects
- Animals, Evolution, Molecular, Opsins genetics, Phylogeny, Water, Coleoptera genetics
- Abstract
In the framework of neutral theory of molecular evolution, genes specific to the development and function of eyes in subterranean animals living in permanent darkness are expected to evolve by relaxed selection, ultimately becoming pseudogenes. However, definitive empirical evidence for the role of neutral processes in the loss of vision over evolutionary time remains controversial. In previous studies, we characterized an assemblage of independently-evolved water beetle (Dytiscidae) species from a subterranean archipelago in Western Australia, where parallel vision and eye loss have occurred. Using a combination of transcriptomics and exon capture, we present evidence of parallel coding sequence decay, resulting from the accumulation of frameshift mutations and premature stop codons, in eight phototransduction genes (arrestins, opsins, ninaC and transient receptor potential channel genes) in 32 subterranean species in contrast to surface species, where these genes have open reading frames. Our results provide strong evidence to support neutral evolutionary processes as a major contributing factor to the loss of phototransduction genes in subterranean animals, with the ultimate fate being the irreversible loss of a light detection system., (Copyright © 2022 Elsevier Inc. All rights reserved.)
- Published
- 2022
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27. Subterranean carbon flows from source to stygofauna: a case study on the atyid shrimp Stygiocaris stylifera (Holthuis, 1960) from Barrow Island (WA).
- Author
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Saccò M, Humphreys WF, Stevens N, Jones MR, Taukulis F, Thomas E, and Blyth AJ
- Subjects
- Animals, Carbon Isotopes analysis, Crustacea, Ecosystem, Food Chain, Invertebrates, Carbon, Groundwater
- Abstract
Groundwater biota are crucial for the ecological functioning of subterranean ecosystems. However, while knowledge of the taxonomic diversity of groundwater invertebrates (stygofauna) is increasing, functional ecological information is still limited. Here, we investigate seldom empirically tested assumptions around stygofaunal trophic plasticity in coping with oligotrophic habitats. We focus on Barrow Island (Western Australia), an ideal natural laboratory due to the occurrence of natural oil seeps in association with aquifers. The trophic position and food source use of the endemic atyid shrimp Stygiocaris stylifera (Holthuis, 1960) were assessed via δ
13 C and δ15 N stable isotope analysis (SIA). Background information on the environmental conditions was gathered through hydrochemical data and δ13 C SIA combined with14 C data from dissolved inorganic/organic carbon and particulate organic carbon from groundwater samples. Our results indicate carbon enrichment in proximity to the natural oil seepage coupled with changes in trophic positions of S. stylifera from higher consumers/predators to biofilm grazers/decomposers. These results are consistent with an increased involvement of hydrocarbon seeps and associated microbial communities in the carbon flows and confirm potential for the trophic flexibility in stygofauna. Further investigations involving other trophic groups will help elucidate the functioning of the ecosystems at a community level.- Published
- 2022
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28. Brazilian cave heritage under siege.
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Ferreira RL, Bernard E, da Cruz Júnior FW, Piló LB, Calux A, Souza-Silva M, Barlow J, Pompeu PS, Cardoso P, Mammola S, García AM, Jeffery WR, Shear W, Medellín RA, Wynne JJ, Borges PAV, Kamimura Y, Pipan T, Hajna NZ, Sendra A, Peck S, Onac BP, Culver DC, Hoch H, Flot JF, Stoch F, Pavlek M, Niemiller ML, Manchi S, Deharveng L, Fenolio D, Calaforra JM, Yager J, Griebler C, Nader FH, Humphreys WF, Hughes AC, Fenton B, Forti P, Sauro F, Veni G, Frumkin A, Gavish-Regev E, Fišer C, Trontelj P, Zagmajster M, Delic T, Galassi DMP, Vaccarelli I, Komnenov M, Gainett G, da Cunha Tavares V, Kováč Ľ, Miller AZ, Yoshizawa K, Di Lorenzo T, Moldovan OT, Sánchez-Fernández D, Moutaouakil S, Howarth F, Bilandžija H, Dražina T, Kuharić N, Butorac V, Lienhard C, Cooper SJB, Eme D, Strauss AM, Saccò M, Zhao Y, Williams P, Tian M, Tanalgo K, Woo KS, Barjakovic M, McCracken GF, Simmons NB, Racey PA, Ford D, Labegalini JA, Colzato N, Ramos Pereira MJ, Aguiar LMS, Moratelli R, Du Preez G, Pérez-González A, Reboleira ASPS, Gunn J, Mc Cartney A, Bobrowiec PED, Milko D, Kinuthia W, Fischer E, Meierhofer MB, and Frick WF
- Published
- 2022
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29. The critical thermal maximum of diving beetles (Coleoptera: Dytiscidae): a comparison of subterranean and surface-dwelling species.
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Jones KK, Humphreys WF, Saccò M, Bertozzi T, Austin AD, and Cooper SJB
- Abstract
Thermal tolerance limits in animals are often thought to be related to temperature and thermal variation in their environment. Recently, there has been a focus on studying upper thermal limits due to the likelihood for climate change to expose more animals to higher temperatures and potentially extinction. Organisms living in underground environments experience reduced temperatures and thermal variation in comparison to species living in surface habitats, but how these impact their thermal tolerance limits are unclear. In this study, we compare the thermal critical maximum (CTmax) of two subterranean diving beetles (Dytiscidae) to that of three related surface-dwelling species. Our results show that subterranean species have a lower CTmax (38.3-39.0°C) than surface species (42.0-44.5°C). The CTmax of subterranean species is ∼10°C higher than the highest temperature recorded within the aquifer. Groundwater temperature varied between 18.4°C and 28.8°C, and changes with time, depth and distance across the aquifer. Seasonal temperature fluctuations were 0.5°C at a single point, with the maximum heating rate being ∼1000x lower (0.008°C/hour) than that recorded in surface habitats (7.98°C/hour). For surface species, CTmax was 7-10°C higher than the maximum temperature in their habitats, with daily fluctuations from ∼1°C to 16°C and extremes of 6.9°C and 34.9°C. These findings suggest that subterranean dytiscid beetles are unlikely to reach their CTmax with a predicted warming of 1.3-5.1°C in the region by 2090. However, the impacts of long-term elevated temperatures on fitness, different life stages and other species in the beetle's trophic food web are unknown., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2021 The Author(s). Published by Elsevier B.V.)
- Published
- 2021
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30. Extreme genetic diversity among springtails (Collembola) in subterranean calcretes of arid Australia.
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Guzik MT, Stevens MI, Cooper SJB, Humphreys WF, and Austin AD
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- Animals, Biodiversity, Calcium Carbonate, Electron Transport Complex IV genetics, Genetic Variation, Phylogeny, Phylogeography, Western Australia, Arthropods classification, Arthropods genetics
- Abstract
The subterranean islands hypothesis for calcretes of the Yilgarn region in Western Australia applies to many stygobitic (subterranean-aquatic) species that are "trapped" evolutionarily within isolated aquifers due to their aquatic lifestyles. In contrast, little is known about the distribution of terrestrial-subterranean invertebrates associated with the calcretes. We used subterranean Collembola from the Yilgarn calcretes to test the hypothesis that troglobitic species, those inhabiting the subterranean unsaturated (non-aquatic) zone of calcretes, are also restricted in their distribution and represent reciprocally monophyletic and endemic lineages. We used the barcoding fragment of the mtDNA cytochrome c oxidase subunit 1 ( COI ) gene from 183 individuals to reconstruct the phylogenetic history of the genus Pseudosinella Schäffer (Collembola, Lepidocyrtidae) from 10 calcretes in the Yilgarn. These calcretes represent less than 5% of the total possible calcretes in this region, yet we show that their diversity for subterranean Collembola comprises a minimum of 25 new species. Regionally, multiple levels of diversity exist in Pseudosinella , indicative of a complex evolutionary history for this genus in the Yilgarn. These species have probably been impacted by climatic oscillations, facilitating their dispersal across the landscape. The results represent a small proportion of the undiscovered diversity in Australia's arid zone.
- Published
- 2021
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31. Rainfall as a trigger of ecological cascade effects in an Australian groundwater ecosystem.
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Saccò M, Blyth AJ, Humphreys WF, Cooper SJB, White NE, Campbell M, Mousavi-Derazmahalleh M, Hua Q, Mazumder D, Smith C, Griebler C, and Grice K
- Abstract
Groundwaters host vital resources playing a key role in the near future. Subterranean fauna and microbes are crucial in regulating organic cycles in environments characterized by low energy and scarce carbon availability. However, our knowledge about the functioning of groundwater ecosystems is limited, despite being increasingly exposed to anthropic impacts and climate change-related processes. In this work we apply novel biochemical and genetic techniques to investigate the ecological dynamics of an Australian calcrete under two contrasting rainfall periods (LR-low rainfall and HR-high rainfall). Our results indicate that the microbial gut community of copepods and amphipods experienced a shift in taxonomic diversity and predicted organic functional metabolic pathways during HR. The HR regime triggered a cascade effect driven by microbes (OM processors) and exploited by copepods and amphipods (primary and secondary consumers), which was finally transferred to the aquatic beetles (top predators). Our findings highlight that rainfall triggers ecological shifts towards more deterministic dynamics, revealing a complex web of interactions in seemingly simple environmental settings. Here we show how a combined isotopic-molecular approach can untangle the mechanisms shaping a calcrete community. This design will help manage and preserve one of the most vital but underrated ecosystems worldwide.
- Published
- 2021
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32. Evidence for speciation underground in diving beetles (Dytiscidae) from a subterranean archipelago.
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Langille BL, Hyde J, Saint KM, Bradford TM, Stringer DN, Tierney SM, Humphreys WF, Austin AD, and Cooper SJB
- Subjects
- Animals, Arrestins genetics, Groundwater, Opsins genetics, Coleoptera genetics, Genetic Drift, Genetic Speciation, Insect Proteins genetics, Vision, Ocular genetics
- Abstract
Most subterranean animals are assumed to have evolved from surface ancestors following colonization of a cave system; however, very few studies have raised the possibility of "subterranean speciation" in underground habitats (i.e., obligate cave-dwelling organisms [troglobionts] descended from troglobiotic ancestors). Numerous endemic subterranean diving beetle species from spatially discrete calcrete aquifers in Western Australia (stygobionts) have evolved independently from surface ancestors; however, several cases of sympatric sister species raise the possibility of subterranean speciation. We tested this hypothesis using vision (phototransduction) genes that are evolving under neutral processes in subterranean species and purifying selection in surface species. Using sequence data from 32 subterranean and five surface species in the genus Paroster (Dytiscidae), we identified deleterious mutations in long wavelength opsin (lwop), arrestin 1 (arr1), and arrestin 2 (arr2) shared by a sympatric sister-species triplet, arr1 shared by a sympatric sister-species pair, and lwop and arr2 shared among closely related species in adjacent calcrete aquifers. In all cases, a common ancestor possessed the function-altering mutations, implying they were already adapted to aphotic environments. Our study represents one of the first confirmed cases of subterranean speciation in cave insects. The assessment of genes undergoing pseudogenization provides a novel way of testing modes of speciation and the history of diversification in blind cave animals., (© 2020 The Authors. Evolution © 2020 The Society for the Study of Evolution.)
- Published
- 2021
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33. Tracking down carbon inputs underground from an arid zone Australian calcrete.
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Saccò M, Blyth AJ, Humphreys WF, Middleton JA, White NE, Campbell M, Mousavi-Derazmahalleh M, Laini A, Hua Q, Meredith K, Cooper SJB, Griebler C, Allard S, Grierson P, and Grice K
- Subjects
- Australia, Carbon Isotopes metabolism, DNA Barcoding, Taxonomic, DNA, Bacterial genetics, DNA, Bacterial isolation & purification, Groundwater microbiology, RNA, Ribosomal, 16S genetics, Rain, Salinity, Soil Microbiology, Spectrometry, Fluorescence, Carbon Cycle, Carbon Isotopes analysis, Environmental Monitoring methods, Groundwater chemistry, Microbiota physiology, Soil chemistry
- Abstract
Freshwater ecosystems play a key role in shaping the global carbon cycle and maintaining the ecological balance that sustains biodiversity worldwide. Surficial water bodies are often interconnected with groundwater, forming a physical continuum, and their interaction has been reported as a crucial driver for organic matter (OM) inputs in groundwater systems. However, despite the growing concerns related to increasing anthropogenic pressure and effects of global change to groundwater environments, our understanding of the dynamics regulating subterranean carbon flows is still sparse. We traced carbon composition and transformations in an arid zone calcrete aquifer using a novel multidisciplinary approach that combined isotopic analyses of dissolved organic carbon (DOC) and inorganic carbon (DIC) (δ13CDOC, δ13CDIC, 14CDOC and 14CDIC) with fluorescence spectroscopy (Chromophoric Dissolved OM (CDOM) characterisation) and metabarcoding analyses (taxonomic and functional genomics on bacterial 16S rRNA). To compare dynamics linked to potential aquifer recharge processes, water samples were collected from two boreholes under contrasting rainfall: low rainfall ((LR), dry season) and high rainfall ((HR), wet season). Our isotopic results indicate limited changes and dominance of modern terrestrial carbon in the upper part (northeast) of the bore field, but correlation between HR and increased old and 13C-enriched DOC in the lower area (southwest). CDOM results show a shift from terrestrially to microbially derived compounds after rainfall in the same lower field bore, which was also sampled for microbial genetics. Functional genomic results showed increased genes coding for degradative pathways-dominated by those related to aromatic compound metabolisms-during HR. Our results indicate that rainfall leads to different responses in different parts of the bore field, with an increase in old carbon sources and microbial processing in the lower part of the field. We hypothesise that this may be due to increasing salinity, either due to mobilisation of Cl- from the soil, or infiltration from the downstream salt lake during HR. This study is the first to use a multi-technique assessment using stable and radioactive isotopes together with functional genomics to probe the principal organic biogeochemical pathways regulating an arid zone calcrete system. Further investigations involving extensive sampling from diverse groundwater ecosystems will allow better understanding of the microbiological pathways sustaining the ecological functioning of subterranean biota., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2020
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34. Refining trophic dynamics through multi-factor Bayesian mixing models: A case study of subterranean beetles.
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Saccò M, Blyth AJ, Humphreys WF, Cooper SJB, Austin AD, Hyde J, Mazumder D, Hua Q, White NE, and Grice K
- Abstract
Food web dynamics are vital in shaping the functional ecology of ecosystems. However, trophic ecology is still in its infancy in groundwater ecosystems due to the cryptic nature of these environments. To unravel trophic interactions between subterranean biota, we applied an interdisciplinary Bayesian mixing model design (multi-factor BMM) based on the integration of faunal C and N bulk tissue stable isotope data (δ
13 C and δ15 N) with radiocarbon data (Δ14 C), and prior information from metagenomic analyses. We further compared outcomes from multi-factor BMM with a conventional isotope double proxy mixing model (SIA BMM), triple proxy (δ13 C, δ15 N, and Δ14 C, multi-proxy BMM), and double proxy combined with DNA prior information (SIA + DNA BMM) designs. Three species of subterranean beetles ( Paroster macrosturtensis , Paroster mesosturtensis, and Paroster microsturtensis ) and their main prey items Chiltoniidae amphipods (AM1: Scutachiltonia axfordi and AM2: Yilgarniella sturtensis ), cyclopoids and harpacticoids from a calcrete in Western Australia were targeted. Diet estimations from stable isotope only models (SIA BMM) indicated homogeneous patterns with modest preferences for amphipods as prey items. Multi-proxy BMM suggested increased-and species-specific-predatory pressures on amphipods coupled with high rates of scavenging/predation on sister species. SIA + DNA BMM showed marked preferences for amphipods AM1 and AM2, and reduced interspecific scavenging/predation on Paroster species. Multi-factorial BMM revealed the most precise estimations (lower overall SD and very marginal beetles' interspecific interactions), indicating consistent preferences for amphipods AM1 in all the beetles' diets. Incorporation of genetic priors allowed crucial refining of the feeding preferences, while integration of more expensive radiocarbon data as a third proxy (when combined with genetic data) produced more precise outcomes but close dietary reconstruction to that from SIA + DNA BMM. Further multidisciplinary modeling from other groundwater environments will help elucidate the potential behind these designs and bring light to the feeding ecology of one the most vital ecosystems worldwide., Competing Interests: None declared., (© 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)- Published
- 2020
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35. Scratching the surface of subterranean biodiversity: Molecular analysis reveals a diverse and previously unknown fauna of Parabathynellidae (Crustacea: Bathynellacea) from the Pilbara, Western Australia.
- Author
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Matthews EF, Abrams KM, Cooper SJB, Huey JA, Hillyer MJ, Humphreys WF, Austin AD, and Guzik MT
- Subjects
- Animals, Biodiversity, Crustacea genetics, Ecosystem, Phylogeny, Western Australia, Crustacea classification
- Abstract
Like other crustacean families, the Parabathynellidae is a poorly studied subterranean and aquatic (stygobiontic) group in Australia, with many regions of available habitat having not yet been surveyed. Here we used a combined approach of molecular species delimitation methods, applied to mitochondrial and nuclear genetic data, to identify putative new species from material obtained from remote subterranean habitats in the Pilbara region of Western Australia. Based on collections from these new localities, we delineated a minimum of eight and up to 24 putative new species using a consensus from a range of molecular delineation methods and additional evidence. When we placed our new putative species into the broader phylogenetic framework of Australian Parabathynellidae, they grouped with two known genera and also within one new and distinct Pilbara-only clade. These new species significantly expand the known diversity of Parabathynellidae in that they represent a 22% increase to the 109 currently recognised species globally. Our investigations showed that sampling at new localities can yield extraordinary levels of new species diversity, with the majority of species showing likely restricted endemic geographical ranges. These findings represent only a small sample from a region comprising less than 2.5% of the Australian continent., (Crown Copyright © 2019. Published by Elsevier Inc. All rights reserved.)
- Published
- 2020
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36. Elucidating stygofaunal trophic web interactions via isotopic ecology.
- Author
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Saccò M, Blyth AJ, Humphreys WF, Kuhl A, Mazumder D, Smith C, and Grice K
- Subjects
- Animals, Australia, Biodiversity, Carbon Isotopes analysis, Nitrogen Isotopes analysis, Aquatic Organisms physiology, Glutamic Acid metabolism, Invertebrates physiology, Phenylalanine metabolism
- Abstract
Subterranean ecosystems host highly adapted aquatic invertebrate biota which play a key role in sustaining groundwater ecological functioning and hydrological dynamics. However, functional biodiversity studies in groundwater environments, the main source of unfrozen freshwater on Earth, are scarce, probably due to the cryptic nature of the systems. To address this, we investigate groundwater trophic ecology via stable isotope analysis, employing δ13C and δ15N in bulk tissues, and amino acids. Specimens were collected from a shallow calcrete aquifer in the arid Yilgarn region of Western Australia: a well-known hot-spot for stygofaunal biodiversity. Sampling campaigns were carried out during dry (low rainfall: LR) and the wet (high rainfall: HR) periods. δ13C values indicate that most of the stygofauna shifted towards more 13C-depleted carbon sources under HR, suggesting a preference for fresher organic matter. Conversion of δ15N values in glutamic acid and phenylalanine to a trophic index showed broadly stable trophic levels with organisms clustering as low-level secondary consumers. However, mixing models indicate that HR conditions trigger changes in dietary preferences, with increasing predation of amphipods by beetle larvae. Overall, stygofauna showed a tendency towards opportunistic and omnivorous habits-typical of an ecologically tolerant community-shaped by bottom-up controls linked with changes in carbon flows. This study provides baseline biochemical and ecological data for stygofaunal trophic interactions in calcretes. Further studies on the carbon inputs and taxa-specific physiology will help refine the interpretation of the energy flows shaping biodiversity in groundwaters. This will aid understanding of groundwater ecosystem functioning and allow modelling of the impact of future climate change factors such as aridification., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2019
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37. Too hot to handle: Cenozoic aridification drives multiple independent incursions of Schizomida (Hubbardiidae) into hypogean environments.
- Author
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Abrams KM, Huey JA, Hillyer MJ, Humphreys WF, Didham RK, and Harvey MS
- Subjects
- Animals, Arachnida genetics, Australia, Base Sequence, Geography, Likelihood Functions, Phylogeny, Time Factors, Arachnida classification, Desert Climate
- Abstract
The formation of the Australian arid zone, Australia's largest and youngest major biome, has been recognized as a major driver of rapid evolutionary radiations in terrestrial plants and animals. Here, we investigate the phylogenetic diversity and evolutionary history of subterranean short-tailed whip scorpions (Schizomida: Hubbardiidae), which are a significant faunal component of Western Australian hypogean ecosystems. We sequenced two mitochondrial (12S, COI) and three nuclear DNA markers (18S, 28S, ITS2) from ∼600 specimens, largely from the genera Draculoides and Paradraculoides, including 20 previously named species and an additional 56 newly identified operational taxonomic units (OTUs). Phylogenetic analyses revealed a large and rapid species radiation congruent with Cenozoic aridification of the continent, in addition to the identification of a new genus in Western Australia and the first epigean schizomid from the Pilbara. Here, we also synonymise Paradraculoides with Draculoides (new synonymy), due to paraphyly and a lack of reliable characters to define the two genera. Our results are consistent with multiple colonisations of the subterranean realm from epigean ancestors as their forest habitat fragmented and retracted, with ongoing fragmentation and diversification of lineages underground. These findings illustrate the remarkable diversity and high incidence of short-range endemism of Western Australia's subterranean fauna, which has important implications for identifying and managing short-range endemic subterranean fauna. They also highlight the advantages of including molecular data in subterranean fauna surveys as all specimens can be utilized, regardless of sex and life stage. Additionally, we have provided the first multi-gene phylogenetic framework for Australian schizomids, which will enable researchers and environmental consultants to identify new taxa or align them to existing lineages., (Copyright © 2019 Elsevier Inc. All rights reserved.)
- Published
- 2019
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38. Shedding light on the hidden world of subterranean fauna: A transdisciplinary research approach.
- Author
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Gibson L, Humphreys WF, Harvey M, Hyder B, and Winzer A
- Subjects
- Animals, Australia, Caves, Interdisciplinary Research, Invertebrates classification, Ecosystem, Groundwater, Invertebrates physiology, Life History Traits
- Abstract
Subterranean environments contain a diverse and unique obligate fauna: either aquatic living in the groundwater or terrestrial living in voids above the water table. In the arid region of the western part of the Australian continent, a particularly rich subterranean fauna coincides with a concentration of natural resource extraction operations. Since the inclusion of subterranean fauna in assessments of environmental impact in the mid-1990s, taxonomic research in Australia on this group of mainly invertebrates has grown exponentially. However, remaining knowledge gaps continue to frustrate both environmental regulators and development proponents due to high uncertainty in the decision-making process. In early 2017, the Western Australian Biodiversity Science Institute was tasked with leading the development of a research program to improve on the current state of knowledge of subterranean fauna. To balance the diverse environmental, economic and social needs of a range of stakeholders, transdisciplinary principles were applied to program development. A clear consensus on five broad focus areas to progress include: (1) data consolidation; (2) resilience to disturbance; (3) survey and sampling protocols; (4) abiotic and biotic habitat requirements; and (5) species delineation. In the context of these focus areas; we describe the research program development, reviewing the status of knowledge within each focus area, and the research initiatives to close the gaps in knowledge. We argue that, by adopting a transdisciplinary approach, the likelihood of success of the research program, as measured by the effective translation and adoption of research findings, will be maximized. This review is timely given the ever-increasing demand on groundwater systems for water extraction worldwide. A holistic understanding of the influence of anthropogenic activities on these ecosystems, and the functional role of organisms within them, will help to ensure that their health is not compromised., (Crown Copyright © 2019. Published by Elsevier B.V. All rights reserved.)
- Published
- 2019
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39. New light in the dark - a proposed multidisciplinary framework for studying functional ecology of groundwater fauna.
- Author
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Saccò M, Blyth A, Bateman PW, Hua Q, Mazumder D, White N, Humphreys WF, Laini A, Griebler C, and Grice K
- Subjects
- Animals, Aquatic Organisms classification, Biodiversity, Carbon Isotopes analysis, Groundwater chemistry, Nitrogen Isotopes analysis, Aquatic Organisms growth & development, Ecology methods, Environmental Monitoring methods, Geologic Sediments chemistry, Groundwater standards
- Abstract
Groundwaters provide the vast majority of unfrozen freshwater resources on the planet, but our knowledge of subsurface ecosystems is surprisingly limited. Stygofauna, or stygobionts -subterranean obligate aquatic animals - provide ecosystem services such as grazing biofilms and maintaining water quality, but we know little about how their ecosystems function. The cryptic nature of groundwaters, together with the high degree of local endemism and stygofaunal site-specific adaptations, represent major obstacles for the field. To overcome these challenges, and integrate biodiversity and ecosystem function, requires a holistic design drawing on classical ecology, taxonomy, molecular ecology and geochemistry. This study presents an approach based on the integration of existing concepts in groundwater ecology with three more novel scientific techniques: compound specific stable isotope analysis (CSIA) of amino acids, radiocarbon analysis (
14 C) and DNA analyses of environmental samples, stygofauna and gut contents. The combination of these techniques allows elucidation of aspects of ecosystem function that are often obscured in small invertebrates and cryptic systems. Carbon (δ13 C) and nitrogen (δ15 N) CSIA provides a linkage between biogeochemical patterns and ecological dynamics. It allows the identification of stygofaunal food web structures and energy flows based on the metabolic pathway of specific amino groups. Concurrently,14 C provides complementary data on the carbon recycling and incorporation within the stygobiotic trophic webs. Changes in groundwater environmental conditions (e.g. aquifer recharge), and subsequent community adaptations, can be pinpointed via the measurementof the radiocarbon fingerprint of water, sediment and specimens. DNA analyses are a rapidly expanding approach in ecology. eDNA is mainly employed as a biomonitoring tool, while metabarcoding of individuals and/or gut contents provides insight into diet regimes. In all cases, the application of the approaches in combination provides more powerful data than any one alone. By combining quantitative (CSIA and14 C) and qualitative (eDNA and DNA metabarcoding) approaches via Bayesian Mixing Models (BMM), linkages can be made between community composition, energy and nutrient sources in the system, and trophic function. This suggested multidisciplinary design will contribute to a more thorough comprehension of the biogeochemical and ecological patterns within these undervalued but essential ecosystems., (Copyright © 2019 Elsevier B.V. All rights reserved.)- Published
- 2019
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40. Sieve-type pore canals in the Timiriaseviinae-A contribution to the comparative morphology and the systematics of the Limnocytheridae (Ostracoda, Crustacea).
- Author
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Danielopol DL, Cabral MC, Lord A, Carbonel P, Gross M, Stoica M, Humphreys WF, Namiotko T, TÓth E, KÜlkÖylÜoĞlu O, Piller WE, and Nunes T
- Subjects
- Animals, Microscopy, Electron, Scanning, Crustacea, Fossils
- Abstract
Examination of normal pore canals, especially sieve-type pore canals, in living and fossil representatives of ten genera of the family Limnocytheridae, subfamily Timiriaseviinae, has revealed important diversity of structure. These complex pore canals have been studied via high-resolution scanning electron microscopy (the Cartographic Method) and analysed via the application of newly devised indices to assess patterns of consistency and variation in both detailed structure of individual pores and of their distribution on the calcified valve. The timiriaseviine taxa are compared with species of the genera Limnocythere, sub-family Limnocytherinae and Cyprideis (family Cytherideidae). The relationship between the living animal and its aquatic environment is discussed in the light of previous studies and of new evidence herein. The importance of normal pore canals for systematics is highlighted by the recognition and definition of the new tribe Gomphodellini Danielopol, Cabral Lord nov. tribe, subfamily Timiriaseviinae, family Limnocytheridae.
- Published
- 2018
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41. Massive Parallel Regression: A Précis of Genetic Mechanisms for Vision Loss in Diving Beetles.
- Author
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Tierney SM, Langille B, Humphreys WF, Austin AD, and Cooper SJB
- Subjects
- Animals, Coleoptera genetics, Ecosystem, Phylogeny, Western Australia, Coleoptera physiology, Evolution, Molecular, Genes, Insect physiology, Vision, Ocular genetics
- Abstract
Two tribes of subterranean dytiscid diving beetles independently colonized groundwater systems of the Western Australian arid zone, a habitat transition that was most likely driven by the contraction of surface water bodies following late Neogene aridification of the Australian continent. These "stygofauna" are now trapped within discrete calcrete aquifers that have formed in paleodrainage valleys, resulting in the world's most diverse radiations of subterranean dytiscid beetles. Approximately 100 species from three genera exhibit partial or fully regressed visual systems and are essentially blind. This unique study system, with multiple independent transitions to subterranean life enables regressive and adaptive evolutionary processes to be studied in parallel at an unheralded comparative scale. Here we provide an overview of the progression of dytiscid beetle research and undertake a literature survey of published research within the field of regressive evolution as it applies to eye loss. We detail our exploration of insect vision genes for signatures of adaptive and neutral evolutionary mechanisms related to eye regression, largely within photoreceptor and eye pigment genes. Our project makes use of transcriptome data from five representative dytiscid beetle species (two surface and three subterranean) in order to design a customized set of RNA baits for use in a hybrid-capture method to target a pool of vision genes sequenced using high-throughput Illumina platforms. This methodological design permits the assessment of modifications in the genomic sequence of beetle vision genes at a much broader scale than Sanger sequencing, enabling a higher number of both target species and genes to be simultaneously assessed relative to research time-investments. Based on our literature search criteria of the research field ("regressive evolution" + "eyes"), 81 papers have been published since the late 1980s accruing an h-index of 27 and a mean citation rate of 24.57. Collective annual citations for this field of research have surged over the past 5 years, an indication that broader scientific community interest is gaining momentum. The majority of publications (75%) have focused on the chordate clade Actinopterygii. Historically, research on variant subterranean taxa has faced difficulties inferring the evolutionary mechanisms of eye regression (and vision loss) using molecular approaches because only a handful of target genes could be feasibly addressed within grant funding cycles. From a comparative phylogenetic perspective, next-generation sequencing approaches applied to stygobiontic dytiscid beetles hold the potential to greatly improve our understanding of the genetic mechanisms underlying regressive evolution generally.
- Published
- 2018
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42. Phylogenetic evidence that both ancient vicariance and dispersal have contributed to the biogeographic patterns of anchialine cave shrimps.
- Author
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Jurado-Rivera JA, Pons J, Alvarez F, Botello A, Humphreys WF, Page TJ, Iliffe TM, Willassen E, Meland K, Juan C, and Jaume D
- Subjects
- Animals, Genes, Mitochondrial, Geography, Crustacea classification, Crustacea genetics, Phylogeny, Phylogeography
- Abstract
Cave shrimps from the genera Typhlatya, Stygiocaris and Typhlopatsa (Atyidae) are restricted to specialised coastal subterranean habitats or nearby freshwaters and have a highly disconnected distribution (Eastern Pacific, Caribbean, Atlantic, Mediterranean, Madagascar, Australia). The combination of a wide distribution and a limited dispersal potential suggests a large-scale process has generated this geographic pattern. Tectonic plates that fragment ancestral ranges (vicariance) has often been assumed to cause this process, with the biota as passive passengers on continental blocks. The ancestors of these cave shrimps are believed to have inhabited the ancient Tethys Sea, with three particular geological events hypothesised to have led to their isolation and divergence; (1) the opening of the Atlantic Ocean, (2) the breakup of Gondwana, and (3) the closure of the Tethys Seaway. We test the relative contribution of vicariance and dispersal in the evolutionary history of this group using mitochondrial genomes to reconstruct phylogenetic and biogeographic scenarios with fossil-based calibrations. Given that the Australia/Madagascar shrimp divergence postdates the Gondwanan breakup, our results suggest both vicariance (the Atlantic opening) and dispersal. The Tethys closure appears not to have been influential, however we hypothesise that changing marine currents had an important early influence on their biogeography.
- Published
- 2017
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43. Taxonomy of Paraplatyarthrus Javidkar and King (Isopoda: Oniscidea: Paraplatyarthridae) with description of five new species from Western Australia, and comments on Australian Trichorhina Budde-Lunde, 1908 (Platyarthridae).
- Author
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Javidkar M, King RA, Cooper SJB, Humphreys WF, and Austin AD
- Subjects
- Animals, Australia, Queensland, Western Australia, Isopoda
- Abstract
The oniscidean fauna of Australia is generally poorly known but recent sampling has revealed a new family, Paraplatyarthridae, found in both terrestrial and groundwater calcretes of central Western Australia. The family was initially described based on a new genus and species, Paraplatyarthrus subterraneus Javidkar and King, 2015. Here we describe an additional five Paraplatyarthrus species from the Yilgarn region of Western Australia, based on both morphological and molecular evidence (COI divergences). Four species are subterranean: P. crebesconiscus Javidkar and King sp. nov., P. cunyuensis Javidkar and King sp. nov., P. occidentoniscus Javidkar and King sp. nov., and P. pallidus Javidkar and King sp. nov., and one is a surface species, P. nahidae Javidkar and King sp. nov. A key to their identification is provided along with information on their distribution. In addition, type material of the two described Australian species of Platyarthridae, Trichorhina australiensis Wahrberg, 1922 from Western Australia and T. tropicalis Lewis, 1998 from Queensland, are examined. Morphological reassessment of type material shows T. australiensis belongs to Paraplatyarthrus (comb. nov.) and that T. tropicalis is correctly placed in Trichorhina, confirming that the genus and family Platyarthridae occur in Australia.
- Published
- 2017
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- View/download PDF
44. Molecular systematics and biodiversity of oniscidean isopods in the groundwater calcretes of central Western Australia.
- Author
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Javidkar M, Cooper SJB, King RA, Humphreys WF, Bertozzi T, Stevens MI, and Austin AD
- Subjects
- Animals, Biodiversity, Cytochromes c classification, Cytochromes c genetics, Cytochromes c metabolism, DNA chemistry, DNA isolation & purification, DNA metabolism, Databases, Genetic, Groundwater parasitology, Isopoda genetics, Lysine-tRNA Ligase classification, Lysine-tRNA Ligase genetics, Lysine-tRNA Ligase metabolism, Phylogeny, RNA, Ribosomal, 18S classification, RNA, Ribosomal, 18S genetics, RNA, Ribosomal, 18S metabolism, RNA, Ribosomal, 28S classification, RNA, Ribosomal, 28S genetics, RNA, Ribosomal, 28S metabolism, Sequence Alignment, Sequence Analysis, DNA, Western Australia, Isopoda classification
- Abstract
Groundwater calcrete aquifers of central Western Australia have been shown to contain a high diversity of stygobiont (subterranean aquatic) invertebrates, with each species confined to an individual calcrete and the entire system resembling a 'subterranean archipelago' containing hundreds of isolated calcretes. Here, we utilised alternative sampling techniques above the water table and uncovered a significant fauna of subterranean terrestrial oniscidean isopods from the calcretes. We explored the diversity and evolution of this fauna using molecular analyses based on one mitochondrial gene, Cytochrome C Oxidase Subunit I (COI), two Ribosomal RNA genes (28S and 18S), and one protein coding nuclear gene, Lysyl-tRNA Synthetase (LysRS). The results from 12 calcretes showed the existence of 36 divergent DNA lineages belonging to four oniscidean families (Paraplatyarthridae, Armadillidae, Stenoniscidae and Philosciidae). Using a combination of phylogenetic and species delimitation methods, we hypothesized the occurrence of at least 27 putative new species of subterranean oniscideans, of which 24 taxa appeared to be restricted to an individual calcrete, lending further support to the "subterranean island hypothesis". Three paraplatyarthrid species were present on adjacent calcretes and these exceptions possessed more ommatidia and body pigments compared with the calcrete-restricted taxa, and are likely to represent troglophiles. The occurrence of stenoniscid isopods in the calcretes of central Western Australia, a group previously only known from the marine littoral zone, suggests a link to the marine inundation of the Eucla basin during the Late Eocene. The current oniscidean subterranean fauna consists of groups known to be subtropical, littoral and benthic, reflecting different historical events that have shaped the evolution of the fauna in the calcretes., (Copyright © 2016 Elsevier Inc. All rights reserved.)
- Published
- 2016
- Full Text
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45. Expansion and Contraction of the Indo-Pacific Tropical Rain Belt over the Last Three Millennia.
- Author
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Denniston RF, Ummenhofer CC, Wanamaker AD, Lachniet MS, Villarini G, Asmerom Y, Polyak VJ, Passaro KJ, Cugley J, Woods D, and Humphreys WF
- Abstract
The seasonal north-south migration of the intertropical convergence zone (ITCZ) defines the tropical rain belt (TRB), a region of enormous terrestrial and marine biodiversity and home to 40% of people on Earth. The TRB is dynamic and has been shown to shift south as a coherent system during periods of Northern Hemisphere cooling. However, recent studies of Indo-Pacific hydroclimate suggest that during the Little Ice Age (LIA; AD 1400-1850), the TRB in this region contracted rather than being displaced uniformly southward. This behaviour is not well understood, particularly during climatic fluctuations less pronounced than those of the LIA, the largest centennial-scale cool period of the last millennium. Here we show that the Indo-Pacific TRB expanded and contracted numerous times over multi-decadal to centennial scales during the last 3,000 yr. By integrating precisely-dated stalagmite records of tropical hydroclimate from southern China with a newly enhanced stalagmite time series from northern Australia, our study reveals a previously unidentified coherence between the austral and boreal summer monsoon. State-of-the-art climate model simulations of the last millennium suggest these are linked to changes in the structure of the regional manifestation of the atmosphere's meridional circulation.
- Published
- 2016
- Full Text
- View/download PDF
46. The Evolution of Epigean and Stygobitic Species of Koonunga Sayce, 1907 (Syncarida: Anaspidacea) in Southern Australia, with the Description of Three New Species.
- Author
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Leijs R, Bradford T, Mitchell JG, Humphreys WF, Cooper SJ, Goonan P, and King RA
- Subjects
- Animals, Australia, Ecosystem, Geography, Phylogeny, Crustacea physiology, Evolution, Molecular
- Abstract
Three new species of Koonunga were discovered in surface and subterranean waters in southern Australia, and were defined using mtDNA analyses and morphology. The new species are: Koonunga hornei Leijs & King; K. tatiaraensis Leijs & King and K. allambiensis Leijs & King. Molecular clock analyses indicate that the divergence times of the species are older than the landscape that they currently inhabit. Different scenarios explaining this apparent discrepancy are discussed in the context of the palaeography of the area. A freshwater epigean origin for Koonunga is considered the most likely hypothesis, whereby some lineages made the transition to the subterranean environment within the last few million years influenced by significant climatic cooling/drying. We discuss the possibility that one stygobitic lineage secondarily regained some of its body pigmentation as adaptation to increased photic conditions after cave collapse and forming of cenotes during the last glacial maximum.
- Published
- 2015
- Full Text
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47. Reply to Nott: Assessing biases in speleothem records of flood events.
- Author
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Denniston RF, Villarini G, Gonzales AN, Polyak VJ, Ummenhofer CC, Lachniet MS, Wanamaker AD Jr, Humphreys WF, Woods D, and Cugley J
- Published
- 2015
- Full Text
- View/download PDF
48. Extreme rainfall activity in the Australian tropics reflects changes in the El Niño/Southern Oscillation over the last two millennia.
- Author
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Denniston RF, Villarini G, Gonzales AN, Wyrwoll KH, Polyak VJ, Ummenhofer CC, Lachniet MS, Wanamaker AD Jr, Humphreys WF, Woods D, and Cugley J
- Abstract
Assessing temporal variability in extreme rainfall events before the historical era is complicated by the sparsity of long-term "direct" storm proxies. Here we present a 2,200-y-long, accurate, and precisely dated record of cave flooding events from the northwest Australian tropics that we interpret, based on an integrated analysis of meteorological data and sediment layers within stalagmites, as representing a proxy for extreme rainfall events derived primarily from tropical cyclones (TCs) and secondarily from the regional summer monsoon. This time series reveals substantial multicentennial variability in extreme rainfall, with elevated occurrence rates characterizing the twentieth century, 850-1450 CE (Common Era), and 50-400 CE; reduced activity marks 1450-1650 CE and 500-850 CE. These trends are similar to reconstructed numbers of TCs in the North Atlantic and Caribbean basins, and they form temporal and spatial patterns best explained by secular changes in the dominant mode of the El Niño/Southern Oscillation (ENSO), the primary driver of modern TC variability. We thus attribute long-term shifts in cyclogenesis in both the central Australian and North Atlantic sectors over the past two millennia to entrenched El Niño or La Niña states of the tropical Pacific. The influence of ENSO on monsoon precipitation in this region of northwest Australia is muted, but ENSO-driven changes to the monsoon may have complemented changes to TC activity.
- Published
- 2015
- Full Text
- View/download PDF
49. Opsin transcripts of predatory diving beetles: a comparison of surface and subterranean photic niches.
- Author
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Tierney SM, Cooper SJ, Saint KM, Bertozzi T, Hyde J, Humphreys WF, and Austin AD
- Abstract
The regressive evolution of eyes has long intrigued biologists yet the genetic underpinnings remain opaque. A system of discrete aquifers in arid Australia provides a powerful comparative means to explore trait regression at the genomic level. Multiple surface ancestors from two tribes of diving beetles (Dytiscidae) repeatedly invaded these calcrete aquifers and convergently evolved eye-less phenotypes. We use this system to assess transcription of opsin photoreceptor genes among the transcriptomes of two surface and three subterranean dytiscid species and test whether these genes have evolved under neutral predictions. Transcripts for UV, long-wavelength and ciliary-type opsins were identified from the surface beetle transcriptomes. Two subterranean beetles showed parallel loss of all opsin transcription, as expected under 'neutral' regressive evolution. The third species Limbodessus palmulaoides retained transcription of a long-wavelength opsin (lwop) orthologue, albeit in an aphotic environment. Tests of selection on lwop indicated no significant differences between transcripts derived from surface and subterranean habitats, with strong evidence for purifying selection acting on L. palmulaoides lwop. Retention of sequence integrity and the lack of evidence for neutral evolution raise the question of whether we have identified a novel pleiotropic role for lwop, or an incipient phase of pseudogene development.
- Published
- 2015
- Full Text
- View/download PDF
50. The linking of plate tectonics and evolutionary divergence.
- Author
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Phillips MJ, Page TJ, de Bruyn M, Huey JA, Humphreys WF, Hughes JM, Santos SR, Schmidt DJ, and Waters JM
- Subjects
- Animals, Amphipoda genetics, Biological Evolution, DNA, Mitochondrial genetics, Ecosystem, Evolution, Molecular, Genome, Mitochondrial, Mitochondrial Proteins genetics
- Published
- 2013
- Full Text
- View/download PDF
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