Mitochondrial DNA supports the identification of two endangered river sharks (Glyphis glyphis and Glyphis garricki) across northern Australia

The river sharks (genus Glyphis) are a small group of poorly known sharks occurring in tropical rivers and estuarine waters across northern Australia, south-east Asia and the subcontinent. The taxonomy of the genus has long been unclear due to very few individuals having been caught and examined, resulting in a paucity of data regarding their distribution, biology and ecology. Only recently has attention focussed on the two Australian species, G. glyphis and G. garricki. This study is a result of a rare opportunity to collate the few samples that have been collected from these species and the bull shark Carcharhinus leucas, which shares an overlapping range. These samples were analysed using the DNA barcoding approach (cox1 mitochondrial gene), compared with six other species of carcharhinids and evaluated in light of the current taxonomic classification. Nine species-specific nucleotide differences were found between G. glyphis and G. garricki and no intra-specific variation provides strong support for the separation into distinct species. Significant differences were also observed at the inter-generic level, with Glyphis forming a distinct clade from Carcharhinus. This study provides the basis for future molecular studies required to better address conservation issues confronting G. glyphis and G. garricki in Australia.

Queensland Coastal Wetland Resources: the Northern Territory Border to Flinders River

Protection of coastal wetland environments is an important prerequisite to effective and sustainable fisheries management and conservation of habitats for the use of future generations. Mangroves, saltmarshes and seagrasses directly support local and offshore fisheries through the provision of food, shelter, breeding and nursery grounds. As such, these vegetated wetland environments along with sandbars, mudflats, rocky foreshores and reefs have significant economic value as well as their intrinsic aesthetic and ecological values. This report summarises the results of the mapping undertaken in the Gulf of Carpentaria Region from the Queensland/Northern Territory border eastwards to the western bank of the Flinders River (hereafter called the Gulf Study Area). The study was undertaken in order to: 1. document and map coastal wetlands of the Gulf Study Area; 2. document levels of existing disturbance to and protection of these wetlands; 3. examine existing recreational, indigenous and commercial fisheries of the region; 4. evaluate the conservation values of the areas investigated from the viewpoint of fisheries productivity and as habitat for important and/or threatened species for future FHA/Marine Protected Area (MPA) declaration. Dataset URL Link: Queensland Coastal Wetlands Resources Mapping data. [Dataset]

Fisheries resources of the Bohle River, Queensland.

The fisheries resources of the Bohle River and its small catchment area adjacent Townsville, north Queensland, were investigated through available literature, scientific research surveys and analysis of commercial and recreational catch and effort data. Research surveys produced a total of 4383 fish from the waters of the Bohle River during 1997-1998. These were classified into 104 fish species from 49 families. Gillnetting, cast netting, fish trapping and crab potting techniques were used in the estuarine waters of the Bohle River with freshwater reaches in the upper catchment surveyed by electrofishing. This range of survey techniques was used to estimate the relative abundance of ten commercially and recreationally important species: Barramundi (Lates calcarifer), king threadfin (Polydactylus macrochir), blue threadfin (Eleutheronema tetradactylum), mangrove jack (Lutjanus argentimaculatus), banded and spotted grunter (Pomadasys kaakan and Pomadasys argenteus), pikey and yellowfin bream (Acanthopagrus berda and Acanthopagrus australis), tilapia (Oreochromis spp.), jungle perch (Kuhlia rupestris) and mud crab (Scylla serrata). The results of each survey method are discussed with a focus on spatial and temporal patterns in diversity and catch rate.

Nutrient loss and water quality under extensive grazing in the upper Burdekin river catchment, North Queensland

Increased sediment and nutrient losses resulting from unsustainable grazing management in the Burdekin River catchment are major threats to water quality in the Great Barrier Reef Lagoon. To test the effects of grazing management on soil and nutrient loss, five 1 ha mini-catchments were established in 1999 under different grazing strategies on a sedimentary landscape near Charters Towers. Reference samples were also collected from watercourses in the Burdekin catchment during major flow events.Soil and nutrient loss were relatively low across all grazing strategies due to a combination of good cover, low slope and low rainfall intensities. Total soil loss varied from 3 to 20 kg haˉ¹ per event while losses of N and P ranged from 10 to 1900 g haˉ¹ and from 1 to 71 g haˉ¹ per event respectively. Water quality of runoff was considered moderate across all strategies with relatively low levels of total suspended sediment (range: 8-1409 mg lˉ¹), total N (range: 101-4000 ug lˉ¹) and total P (range: 14-609 ug lˉ¹). However, treatment differences are likely to emerge with time as the impacts of the different grazing strategies on land condition become more apparent.Samples collected opportunistically from rivers and creeks during flow events displayed significantly higher levels of total suspended sediment (range: 10-6010 mg lˉ¹), total N (range: 650-6350 ug lˉ¹) and total P (range: 50-1500 ug lˉ¹) than those collected at the grazing trial. These differences can largely be attributed to variation in slope, geology and cover between the grazing trial and different catchments. In particular, watercourses draining hillier, grano-diorite landscapes with low cover had markedly higher sediment and nutrient loads compared to those draining flatter, sedimentary landscapes.These preliminary data suggest that on relatively flat, sedimentary landscapes, extensive cattle grazing is compatible with achieving water quality targets, provided high levels of ground cover are maintained. In contrast, sediment and nutrient loss under grazing on more erodable land types is cause for serious concern. Long-term empirical research and monitoring will be essential to quantify the impacts of changed land management on water quality in the spatially and temporally variable Burdekin River catchment.

Economic case study of ABCD cane management practices in the Burdekin River Irrigation Area (BRIA) region

A case study was undertaken to determine the economic impact of a change in management class as detailed in the A, B, C and D management class framework. This document focuses on the implications of changing from D to C, C to B and B to A class management in the Burdekin River irrigation area (BRIA) and if the change is worthwhile from an economic perspective. This report provides a guide to the economic impact that may be expected when undertaking a particular change in farming practices and will ultimately lead to more informed decisions being made by key industry stakeholders. It is recognised that these management classes have certain limitations and in many cases the grouping of practices may not be reflective of the real situation. The economic case study is based on the A, B, C and D management class framework for water quality improvement developed in 2007/2008 for the Burdekin natural resource management region. The framework for the Burdekin is currently being updated to clarify some issues and incorporate new knowledge since the earlier version of the framework. However, this updated version is not yet complete and so the Paddock to Reef project has used the most current available version of the framework for the modelling and economics. As part of the project specification, sugarcane crop production data for the BRIA was provided by the APSIM model. The information obtained from the APSIM crop modelling programme included sugarcane yields and legume grain yield (legume grain yield only applies to A class management practice). Because of the complexity involved in the economic calculations, a combination of the FEAT, PiRisk and a custom made spreadsheet was used for the economic analysis. Figures calculated in the FEAT program were transferred to the custom made spreadsheet to develop a discounted cash flow analysis. The marginal cash flow differences for each farming system were simulated over a 5-year and 10-year planning horizon to determine the net present value of changing across different management practices. PiRisk was used to test uncertain parameters in the economic analysis and the potential risk associated with a change in value.

Paddock to Reef Monitoring & Evaluation - Economic analysis of ‘ABCD’ cane management for the Burdekin River Irrigation Area.

The economic analysis is based on the A, B, C and D management practice framework for water quality improvement developed in 2007/2008 by the respective natural resource management region. This document focuses on the economic implications of these management practices in the Burdekin River Irrigation Area (BRIA). A review of the management practices is currently being undertaken to clarify some issues and incorporate new knowledge since the earlier version of the framework. However, this updated version is not yet complete and so the Paddock to Reef project has used the most current available version of the framework for the modelling and economics.

Fish mediate high food web connectivity in the lower reaches of a tropical floodplain river

High levels of hydrological connectivity during seasonal flooding provide significant opportunities for movements of fish between rivers and their floodplains, estuaries and the sea, possibly mediating food web subsidies among habitats. To determine the degree of utilisation of food sources from different habitats in a tropical river with a short floodplain inundation duration (similar to 2 months), stable isotope ratios in fishes and their available food were measured from three habitats (inundated floodplain, dry season freshwater, coastal marine) in the lower reaches of the Mitchell River, Queensland (Australia). Floodplain food sources constituted the majority of the diet of large-bodied fishes (barramundi Lates calcarifer, catfish Neoarius graeffei) captured on the floodplain in the wet season and for gonadal tissues of a common herbivorous fish (gizzard shad Nematalosa come), the latter suggesting that critical reproductive phases are fuelled by floodplain production. Floodplain food sources also subsidised barramundi from the recreational fishery in adjacent coastal and estuarine areas, and the broader fish community from a freshwater lagoon. These findings highlight the importance of the floodplain in supporting the production of large fishes in spite of the episodic nature and relatively short duration of inundation compared to large river floodplains of humid tropical regions. They also illustrate the high degree of food web connectivity mediated by mobile fish in this system in the absence of human modification, and point to the potential consequences of water resource development that may reduce or eliminate hydrological connectivity between the river and its floodplain.

Demonstration reaches: Looking back whilst moving forward with river rehabilitation under the Native Fish Strategy

‘Demonstration reaches’ are sections of river where multiple threats to native fish are addressed through river rehabilitation and strong community participation. They are an important way of promoting the key driving actions of the Murray-Darling Basin Authority's Native Fish Strategy (NFS) by using on-ground community-driven rehabilitation. Measuring rehabilitation success against well-defined targets and using this information to adaptively mange activities is fundamental to the demonstration reach philosophy. Seven years on from the establishment of the first demonstration reach, there are now seven throughout the Murray-Darling Basin (MDB), all in differing states of maturation and but all applying a standardised framework for monitoring native fish outcomes. In this study, we reflect on the role that demonstration reaches have played within the NFS, synthesise some key findings from 32 monitoring and evaluation outputs, and highlight some of the successes and barriers to success. We make recommendations as to how to strengthen the demonstration reach model to ensure it remains a relevant approach for fish habitat rehabilitation beyond the NFS and MDB.

Variation in the hindgut microbial communities of the Florida manatee, Trichechus manatus latirostris over winter in Crystal River, Florida

The Florida manatee, Trichechus manatus latirostris, is a hindgut-fermenting herbivore. In winter, manatees migrate to warm water overwintering sites where they undergo dietary shifts and may suffer from cold-induced stress. Given these seasonally induced changes in diet, the present study aimed to examine variation in the hindgut bacterial communities of wild manatees overwintering at Crystal River, west Florida. Faeces were sampled from 36 manatees of known sex and body size in early winter when manatees were newly arrived and then in mid-winter and late winter when diet had probably changed and environmental stress may have increased. Concentrations of faecal cortisol metabolite, an indicator of a stress response, were measured by enzyme immunoassay. Using 454-pyrosequencing, 2027 bacterial operational taxonomic units were identified in manatee faeces following amplicon pyrosequencing of the 16S rRNA gene V3/V4 region. Classified sequences were assigned to eight previously described bacterial phyla; only 0.36% of sequences could not be classified to phylum level. Five core phyla were identified in all samples. The majority (96.8%) of sequences were classified as Firmicutes (77.3 ± 11.1% of total sequences) or Bacteroidetes (19.5 ± 10.6%). Alpha-diversity measures trended towards higher diversity of hindgut microbiota in manatees in mid-winter compared to early and late winter. Beta-diversity measures, analysed through permanova, also indicated significant differences in bacterial communities based on the season.

Optimizing sowing management for short duration dry seeded aman rice on the High Ganges River Floodplain of Bangladesh

Dry seeding of aman rice can facilitate timely crop establishment and early harvest and thus help to alleviate the monga (hunger) period in the High Ganges Flood Plain of Bangladesh. Dry seeding also offers many other potential benefits, including reduced cost of crop establishment and improved soil structure for crops grown in rotation with rice. However, the optimum time for seeding in areas where farmers have access to water for supplementary irrigation has not been determined. We hypothesized that earlier sowing is safer, and that increasing seed rate mitigates the adverse effects of significant rain after sowing on establishment and crop performance. To test these hypotheses, we analyzed long term rainfall data, and conducted field experiments on the effects of sowing date (target dates of 25 May, 10 June, 25 June, and 10 July) and seed rate (20, 40, and 60 kg ha−1) on crop establishment, growth, and yield of dry seeded Binadhan-7 (short duration, 110–120 d) during the 2012 and 2013 rainy seasons. Wet soil as a result of untimely rainfall usually prevented sowing on the last two target dates in both years, but not on the first two dates. Rainfall analysis also suggested a high probability of being able to dry seed in late May/early June, and a low probability of being able to dry seed in late June/early July. Delaying sowing from 25 May/10 June to late June/early July usually resulted in 20–25% lower plant density and lower uniformity of the plant stand as a result of rain shortly after sowing. Delaying sowing also reduced crop duration, and tillering or biomass production when using a low seed rate. For the late June/early July sowings, there was a strong positive relationship between plant density and yield, but this was not the case for earlier sowings. Thus, increasing seed rate compensated for the adverse effect of untimely rains after sowing on plant density and the shorter growth duration of the late sown crops. The results indicate that in this region, the optimum date for sowing dry seeded rice is late May to early June with a seed rate of 40 kg ha−1. Planting can be delayed to late June/early July with no yield loss using a seed rate of 60 kg ha−1, but in many years, the soil is simply too wet to be able to dry seed at this time due to rainfall.

Optimisation of in-cell accelerated solvent extraction technique for the determination of organochlorine pesticides in river sediments

Organochlorine pesticides (OCPs) are ubiquitous environmental contaminants with adverse impacts on aquatic biota, wildlife and human health even at low concentrations. However, conventional methods for their determination in river sediments are resource intensive. This paper presents an approach that is rapid and also reliable for the detection of OCPs. Accelerated Solvent Extraction (ASE) with in-cell silica gel clean-up followed by Triple Quadrupole Gas Chromatograph Mass Spectrometry (GCMS/MS) was used to recover OCPs from sediment samples. Variables such as temperature, solvent ratio, adsorbent mass and extraction cycle were evaluated and optimised for the extraction. With the exception of Aldrin, which was unaffected by any of the variables evaluated, the recovery of OCPs from sediment samples was largely influenced by solvent ratio and adsorbent mass and, to some extent, the number of cycles and temperature. The optimised conditions for OCPs extraction in sediment with good recoveries were determined to be 4 cycles, 4.5 g of silica gel, 105 ᴼC, and 4:3 v/v DCM: hexane mixture. With the exception of two compounds (α-BHC and Aldrin) whose recoveries were low (59.73 and 47.66 % respectively), the recovery of the other pesticides were in the range 85.35 – 117.97% with precision < 10 % RSD. The method developed significantly reduces sample preparation time, the amount of solvent used, matrix interference, and is highly sensitive and selective.

Identifying the Influence of Channel Morphology on Physical Habitat Availability for Native Fish: Application to the Two-spined Blackfish (Gadopsis bispinosus) in the Cotter River, Australia.

The impact of channel morphology and flow on physical habitat availability for the two-spined blackfish (Gadopsis bispinosus) was assessed in the Cotter River, ACT, Australia. Physical habitat requirements for three life stages were identified based on previous field sampling in the Cotter River. Two sites were selected with contrasting channel morphology: Spur Hole, with a moderate gradient and runs and glides, and Vanity’s Crossing, with a steeper gradient, rapids, and fast-flowing pools. Physical Habitat Simulation System (PHABSIM) was used to simulate the flow v. physical habitat availability relationship for each life stage at both sites. Clear differences were apparent between sites, with Spur Hole characterised by increasing habitat with increasing flow and Vanity’s Crossing showing the opposite relationship. The nature of the channel morphology determined this difference, with Spur Hole characterised by marginal zones becoming inundated at higher flows and providing additional suitable physical habitat as discharge increases. Vanity’s Crossing does not contain similar marginal zones. Further analysis demonstrated that high water velocity was the most important factor limiting physical habitat availability at both sites. This approach demonstrates the importance of channel morphology in determining physical habitat availability and an alternative use of PHABSIM to highlight limiting factors for target species.

Le site CjEd-8 : l'Archaïque supérieur au Témiscouata

Occupé depuis près de 10 000 ans, le Témiscouata est un lieu clé pour mieux comprendre la préhistoire du Québec, en raison de son emplacement stratégique entre l’Atlantique et la vallée du Saint-Laurent et de la cinquantaine de sites archéologiques connus dans la région. Le site CjEd-8 est le seul site associé à l’Archaïque supérieur (6 000 à 4 000 ans avant aujourd’hui) connu dans la région. Cette recherche palethnographique porte sur l’analyse de la collection lithique du site archéologique CjEd-8. Nos questions de recherche sont les suivantes : quel était le mode de vie et les activités des occupants du site CjEd-8? Quel était leur environnement et comment s’y sont-ils adapté? Comment l’espace était-il utilisé sur le site? Comment ce site se compare-t-il aux autres sites de l’Archaïque supérieur au Québec et dans le nord-est américain? Est-il possible de relier l’occupation du site CjEd-8 à un plus vaste cadre régional ou culturel, comme un réseau d’interaction, par exemple? Nous avons effectué une analyse techno-morphologique individuelle de tous les outils et du débitage de la collection. Nous avons pu constater que tous les stades de réduction lithique (initial, intermédiaire et final) sont présents sur le site CjEd-8. Les matières premières locales sont représentées dans tous ces stades de réduction, bien que les matières premières exotiques soient surtout présentes au sein du stade initial de réduction, davantage que les matières premières locales. Ceci laisse croire que le dégrossissement initial des blocs et galets de matière première locale se faisait ailleurs que sur le site, fort probablement sur les carrières de chert de la région, et que des matières exotiques ont aussi été travaillées sur le site. Des activités de taille ont eu lieu sur les deux zones du site, probablement autour de deux foyers distincts. Les quelques individus présents y sont demeurés très brièvement, semblent avoir effectué un nombre limité d’activités et sont peut-être repassés quelques temps après. L’Archaïque supérieur est caractérisé par une augmentation de la population et par l’intensification des interactions et de l’appartenance régionale. Or, il semblerait que ce soit l’inverse que l’on observe archéologiquement au Témiscouata. L’assemblage de CjEd-8 ne présente aucune ressemblance particulière avec les sites associés à l’Archaïque supérieur au Québec, bien que pour presque tous ces sites, on constate une exploitation importante des matières premières locales (même si ces dernières sont de qualité moyenne), combinée à l’exploitation de matières premières exotiques de sources très éloignées. L’industrie du quartz, importante dans la plupart des sites de l’Archaïque supérieur, se reflète très peu sur CjEd-8. Bien qu’il nous soit impossible d’associer l’occupation du site CjEd-8 à une tradition culturelle précise, cela ne signifie pas que ses occupants n’étaient pas en interaction avec l’une ou l’autre des entités culturelles de la fin de l’Archaïque, que ce soit avec les groupes de la région de Quoddy, de la Gaspésie, de la Vallée du Saint-Laurent, de l’Outaouais, de la Haute Côte nord, du Vermont, de l’État de New York et de l’intérieur du Maine. La question des modes de subsistance des occupants de CjEd-8 n’a pas été soulevée lors de nos analyses. Nous savons toutefois que les occupants du Témiscouata avaient alors accès à une faune riche et diversifiée.

L’exploitation du phoque dans le secteur de l’embouchure du Saguenay (Québec, Canada) par les Iroquoiens au Sylvicole supérieur(1000-1534 de notre ère)

Au cours du Sylvicole supérieur (1000-1500 AD), le secteur de l’embouchure du Saguenay aurait été exploité par des groupes Iroquoiens du Saint-Laurent en quête de ressources marines, et plus particulièrement du phoque. Ces groupes provenaient vraisemblablement de la région de Québec où se trouvaient leurs camps de base et auraient ainsi développé une forme d’adaptation aux ressources marines de l’estuaire, faisant d’eux les groupes iroquoiens les plus mobiles de toute la vallée du Saint-Laurent. Dans cette étude, nous proposons que l’exploitation des mammifères marins fût pratiquée en deux temps, d’abord au printemps, lors de courtes périodes par des contignents de chasseurs masculins attirés par le phoque du Groenland et puis en été, par des familles entières profitant de la présence de phoques gris et commun. Les pinnipèdes étaient probablement traqués sur la batture ou sur les glaces et abattus à la hache ou à l’arc et à la flèche. Puisque les résidus alimentaires retrouvés dans les vases de cuisson étaient surtout composés de poissons et de mammifères terrestres, il est supposé que des sous-produits de la chasse au phoque aient été rapportés dans la région de Québec et utilisés comme réserve de nourriture, comme matière première ou comme monnaie d’échange. Nous défendons également l’hypothèse que ces excursions dans l’estuaire n’étaient pas nécessairement liées à la précarité de l’agriculture dans la région de Québec puisque cette pratique aurait été adoptée tardivement, soit après 1300 AD et peut être même à partir de 1400 AD. Les données sont issues de six sites ayant fait l’objet de fouilles répartis sur une bande littorale de 40 km de longueur. Il s’agit des sites Ouellet (DaEk-6), Anse-aux-Pilotes IV (DbEj-7), Cap-de-Bon-Désir (109G), Site archéologique des Basques-de-l’Anse-à-la-Cave (DbEi-5), Pointe-à-Crapaud (DbEi-2) et Escoumins I (DcEi-1).

Redevances forestièrse annuelles et développement local au Cameroun : expériences de deux communes rurales : une analyse anthropologique

Notre thèse étudie les liens entre les « redevances forestières annuelles » (RFA) et le « développement local » dans deux communes du Cameroun. Ce travail anthropologique s’inscrit dans le débat qui se fait à l’échelle internationale relativement au rôle et au devenir des populations locales dans la gestion des ressources naturelles. Dans le passé, la gestion des redevances forestières annuelles (RFA) a été, dans les pays d’Afrique centrale et au Cameroun en particulier, sous la seule responsabilité de l’État central. Une telle politique n’offrait pas la garantie nécessaire à l’utilisation durable de ces ressources qui sont indispensables à la vie des populations villageoises riveraines et à l’équilibre de l’environnement. Profitant de la crise des années 1980 et 1990 en Afrique, le FMI et la Banque mondiale ont exercé une pression sur les États africains pour qu’ils revoient, en conformité avec la Conférence de Rio (1992), leurs politiques en matière de gestion et de conservation des ressources forestières. Dans le bassin du Congo, le Cameroun a été le tout premier pays à réviser, en 1994, ses lois forestières par le biais d’une décentralisation de la fiscalité forestière : les taxes perçues furent réparties entre l’État, les collectivités territoriales décentralisées et les populations villageoises riveraines. Les fonds transférés aux communes et aux populations riveraines devaient servir au développement local en contribuant notamment à l’amélioration des conditions générales de vie des populations à travers la réalisation d’œuvres sociales, l’adduction d’eau, la construction et l’entretien des routes, des écoles, des cases de santé, etc. Dans les faits, l’impact de la fiscalité forestière décentralisée reste à ce jour encore peu visible sur la dynamique du développement local des communes. Notre projet de recherche doctorale prend place dans le domaine d’une anthropologie du développement centrée sur l’étude des solutions que les populations locales apportent aux problèmes auxquels elles sont confrontées dans leur vie de tous les jours. L’analyse des impacts que les politiques de développement économique exercent sur les populations villageoises d’Afrique est ici à l’avant-plan, pas seulement au sens d’une critique des politiques étatiques en matière d’exploitation forestière, mais aussi au sens d’une meilleure compréhension des conditions de mise en œuvre de ces politiques et de l’impact de celles-ci sur les populations villageoises, tant sur le plan des avantages financiers directs que des transformations écologiques que les activités forestières introduisent dans les pratiques agricoles des villageois. Sur le plan méthodologique, il faut noter que ce fut très difficile d’obtenir les informations nécessaires, notre sujet d’étude se révélant être très sensible quant à sa portée politique. Nous avons néanmoins pu recueillir un solide ensemble de données par le biais d’une démarche de proximité de type qualitatif qui a été conduite dans deux communes forestières qui représentent deux réalités différentes en matière de gestion des RFA. La collecte des données a été faite, de manière intensive, dans sept villages qui répondaient à nos critères : nous avons ainsi pu étudier, de manière approfondie, la situation des groupes sociaux les plus défavorisés qui sont exclus dans le partage des revenus forestiers. Pour construire notre cadre théorique, nous avons combiné des éléments empruntés aux théories environnementales, à l’anthropologie économique et à l’analyse des modes de gestion. Il faut noter, par ailleurs, que l’anthropologue n’est ni un aménagiste, ni un environnementaliste, ni un spécialiste des études managériales. Nous avons conduit notre étude comparative dans les communes concernées en nous fixant pour objectif de comprendre les mécanismes de gestion des RFA mis en place par les leaders locaux et d’évaluer leur impact sur l’amélioration des conditions de vie des populations villageoises et sur leur écosystème. Notre préoccupation était de savoir si les RFA constituent des vecteurs de développement socioéconomique pour des populations vivant dans et de la forêt.