Pepperell Research and Consulting Pty Ltd

Box Hill South, Australia

Pepperell Research and Consulting Pty Ltd

Box Hill South, Australia

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Griffiths S.P.,CSIRO | Pollock K.H.,Murdoch University | Lyle J.M.,University of Tasmania | Pepperell J.G.,Pepperell Research and Consulting Pty Ltd | And 2 more authors.
Fish and Fisheries | Year: 2010

Obtaining reliable estimates of important parameters from recreational fisheries is problematic but critical for stock assessment and effective resource management. Sampling methodologies based on traditional design-based sampling theory, is inadequate in obtaining representative catch and effort data, social or demographical characterization, or fisher behaviour from small hard-to-reach components within recreational fisheries (e.g. specialized sport fisheries) that may account for the majority of the catch for some species. A model-based approach to sampling is necessary. Researchers in other disciplines including epidemiology and social sciences routinely survey rare or 'hidden' populations within the general community by penetration of social networks rather than by interception of individuals. We encourage fisheries researchers to rethink survey designs and consider the social elements of recreational fishing. Employing chain-referral methods, such as respondent-driven sampling (RDS), may be a statistically robust and cost-effective option for sampling elusive sub-elements within recreational fisheries. Chain-referral sampling methodology is outlined and an example of a complemented 'RDS-recapture' survey design is introduced as a cost-effective application to estimating total catch in recreational fisheries. © 2010 Blackwell Publishing Ltd.


Williams S.M.,University of Queensland | Holmes B.J.,University of Queensland | Pepperell J.G.,Pepperell Research and Consulting Pty Ltd
PLoS ONE | Year: 2015

Increasing fishing pressure and uncertainty surrounding recreational fishing catch and effort data promoted the development of alternative methods for conducting fisheries research. A pilot investigation was undertaken to engage the Australian game fishing community and promote the non-lethal collection of tissue samples from the black marlin Istiompax indica, a valuable recreational-only species in Australian waters, for the purpose of future genetic research. Recruitment of recreational anglers was achieved by publicizing the project in magazines, local newspapers, social media, blogs, websites and direct communication workshops at game fishing tournaments. The Game Fishing Association of Australia and the Queensland Game Fishing Association were also engaged to advertise the project and recruit participants with a focus on those anglers already involved in the tag-and-release of marlin. Participants of the program took small tissue samples using non-lethal methods which were stored for future genetic analysis. The program resulted in 165 samples from 49 participants across the known distribution of I. indica within Australian waters which was a sufficient number to facilitate a downstream population genetic analysis. The project demonstrated the potential for the development of citizen science sampling programs to collect tissue samples using non-lethal methods in order to achieve targeted research objects in recreationally caught species. © 2015 Williams et al.


Griffiths S.P.,CSIRO | Zischke M.T.,University of Queensland | Tonks M.L.,CSIRO | Pepperell J.G.,Pepperell Research and Consulting Pty Ltd | Tickell S.,CSIRO
Reviews in Fish Biology and Fisheries | Year: 2013

Advances in fishing technologies have increased the efficiency and diversification of recreational fisheries. This poses challenges for surveying specialised or 'hard-to-reach' recreational fishers (e.g. sport fishers) that may take the majority of the recreational catch for some species, but are too rare within the general population to be sampled cost-effectively using existing methods. We trialled two new methods-time-location sampling (TLS) and online diaries-for surveying specialised recreational longtail tuna (Thunnus tonggol) fishers. Results were compared with a concurrent traditional access point survey (APS). Online diaries were inexpensive but unsuitable for collecting representative data due to avidity, volunteerism, and differential recruitment bias. APS yielded high resolution data on catch, effort and size composition but was expensive and ineffective for sampling all components of the fishery. In contrast, TLS conducted at fishing tackle stores was cost-effective for accessing the breadth of fisher types due to the need for all fishers to purchase or to inspect fishing-related products at some point. Given the frequent absence of complete list frames for recreational fisheries, we suggest undertaking multiple TLS surveys to collect catch rate data and to simultaneously estimate population size using capture-recapture approaches in order to estimate the total recreational catch of species of interest. © 2012 Springer Science+Business Media Dordrecht.


Kopf R.K.,Charles Sturt University | Davie P.S.,Massey University | Bromhead D.,British Petroleum | Pepperell J.G.,Pepperell Research and Consulting Pty. Ltd.
ICES Journal of Marine Science | Year: 2011

This study describes the first validated model of age and growth developed for striped marlin (Kajikia audax). Daily periodicity of otolith microincrements was corroborated by back-calculated hatch dates that matched the known spawning season in the Southwest Pacific Ocean (SWPO). Yearly annulus formation in fin-spine sections was corroborated by daily otolith microincrements and by a marginal increment analysis. Ages of females ranged from 140 d to 8.5 years in fish between 990 mm and 2872 mm lower-jaw fork length (LJFL), and ages of males from 130 d to 7.0 years in fish between 1120 mm and 2540 mm LJFL. Sex-specific differences in growth were significant, with females growing to a larger asymptotic size and greater age than males. An instantaneous growth rate of 3.1 mm d -1 at 6 months and an estimated length of 1422-1674 mm LJFL by age 1 year makes this species among the fastest growing bony fish. Implications of these findings are discussed in relation to commercial longline and recreational fisheries management of striped marlin in the SWPO and in relation to the biology of pelagic fish growth. © 2011 International Council for the Exploration of the Sea.


Williams S.M.,University of Queensland | Pepperell J.G.,Pepperell Research and Consulting Pty Ltd. | Corley S.W.,University of Queensland | Ovenden J.R.,University of Queensland
Fisheries Research | Year: 2015

We present the isolation and characterisation of 18 polymorphic microsatellite loci with perfect 3 and 4-bp repeats for the black marlin Istiompax indica using Ion Torrent next-generation sequencing techniques. Usefulness of these markers for genetic studies was assessed by screening 16 specimens collected throughout the Indo-Pacific basin for this broadly distributed and exploited species. A total of 30 black marlin from the West Coral Sea were genotyped producing between 2 and 20 alleles per locus (mean 5.27) with expected heterozygosity (HE) ranging from 0.095 to 0.843. The genotypic distribution of all loci conformed to Hardy-Weinberg expectations with no evidence of null alleles. Evaluations of cross-species amplification of these markers on five additional Pacific billfish species indicates the utility of these markers for genetic studies of other Istiophorids. © 2014 Elsevier B.V.


Hill N.J.,James Cook University | Tobin A.J.,James Cook University | Reside A.E.,James Cook University | Pepperell J.G.,Pepperell Research and Consulting Pty Ltd. | And 2 more authors.
Global Change Biology | Year: 2016

Many taxa are undergoing distribution shifts in response to anthropogenic climate change. However, detecting a climate signal in mobile species is difficult due to their wide-ranging, patchy distributions, often driven by natural climate variability. For example, difficulties associated with assessing pelagic fish distributions have rendered fisheries management ill-equipped to adapt to the challenges posed by climate change, leaving pelagic species and ecosystems vulnerable. Here, we demonstrate the value of citizen science data for modelling the dynamic habitat suitability of a mobile pelagic predator (black marlin, Istiompax indica) within the south-west Pacific Ocean. The extensive spatial and temporal coverage of our occurrence data set (n = 18 717), collected at high resolution (~1.85 km2), enabled identification of suitable habitat at monthly time steps over a 16-year period (1998-2013). We identified considerable monthly, seasonal and interannual variability in the extent and distribution of suitable habitat, predominately driven by chlorophyll a and sea surface height. Interannual variability correlated with El Nino Southern Oscillation (ENSO) events, with suitable habitat extending up to ~300 km further south during La Nina events. Despite the strong influence of ENSO, our model revealed a rapid poleward shift in the geometric mean of black marlin habitat, occurring at 88.2 km decade-1. By incorporating multiple environmental factors at monthly time steps, we were able to demonstrate a rapid distribution shift in a mobile pelagic species. Our findings suggest that the rapid velocity of climate change in the south-west Pacific Ocean is likely affecting mobile pelagic species, indicating that they may be more vulnerable to climate change than previously thought. © 2016 John Wiley & Sons Ltd.


Holmes B.J.,University of Queensland | Pepperell J.G.,Pepperell Research and Consulting Pty Ltd | Griffiths S.P.,CSIRO | Jaine F.R.A.,University of Queensland | And 3 more authors.
Marine Biology | Year: 2014

Partial migration is considered ubiquitous among vertebrates, but little is known about the movements of oceanodromous apex predators such as sharks, particularly at their range extents. PAT-Mk10 and SPOT5 electronic tags were used to investigate tiger shark (Galeocerdo cuvier) spatial dynamics, site fidelity and habitat use off eastern Australia between April 2007 and May 2013. Of the 18 tags deployed, 15 recorded information on depth and/or temperature, and horizontal movements. Tracking times ranged between four and 408 days, with two recovered pop-up archival tags allowing 63 days of high-resolution archived data to be analysed. Overall mean proportions of time-at-depth revealed that G. cuvier spent the majority of time-at-depths of <20 m, but undertook dives as deep as 920 m. Tagged sharks occupied ambient water temperatures from 29.5 °C at the surface to 5.9 °C at depth. Deep dives (>500 m) occurred mostly around dawn and dusk, but no definitive daily dive patterns were observed. Horizontal movements were characterised by combinations of resident and transient behaviour that coincided with seasonal changes in water temperature. While the majority of movement activity was focused around continental slope waters, large-scale migration was evident with one individual moving from offshore Sydney, Australia, to New Caledonia (c. 1,800 km) in 48 days. Periods of tiger shark residency outside of Australia’s fisheries management zones highlight the potential vulnerability of the species to unregulated fisheries and the importance of cross-jurisdictional arrangements for species’ management and conservation. © 2014, Springer-Verlag Berlin Heidelberg.


PubMed | Pepperell Research and Consulting Pty Ltd. and James Cook University
Type: Journal Article | Journal: Global change biology | Year: 2016

Many taxa are undergoing distribution shifts in response to anthropogenic climate change. However, detecting a climate signal in mobile species is difficult due to their wide-ranging, patchy distributions, often driven by natural climate variability. For example, difficulties associated with assessing pelagic fish distributions have rendered fisheries management ill-equipped to adapt to the challenges posed by climate change, leaving pelagic species and ecosystems vulnerable. Here, we demonstrate the value of citizen science data for modelling the dynamic habitat suitability of a mobile pelagic predator (black marlin, Istiompax indica) within the south-west Pacific Ocean. The extensive spatial and temporal coverage of our occurrence data set (n=18717), collected at high resolution (~1.85km(2) ), enabled identification of suitable habitat at monthly time steps over a 16-year period (1998-2013). We identified considerable monthly, seasonal and interannual variability in the extent and distribution of suitable habitat, predominately driven by chlorophyll a and sea surface height. Interannual variability correlated with El Nino Southern Oscillation (ENSO) events, with suitable habitat extending up to ~300km further south during La Nina events. Despite the strong influence of ENSO, our model revealed a rapid poleward shift in the geometric mean of black marlin habitat, occurring at 88.2kmdecade(-1) . By incorporating multiple environmental factors at monthly time steps, we were able to demonstrate a rapid distribution shift in a mobile pelagic species. Our findings suggest that the rapid velocity of climate change in the south-west Pacific Ocean is likely affecting mobile pelagic species, indicating that they may be more vulnerable to climate change than previously thought.


PubMed | University of Queensland, Pepperell Research and Consulting Pty Ltd and Technical University of Denmark
Type: | Journal: Molecular ecology resources | Year: 2016

Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant archived skeletal material from sharks as a source of DNA for temporal genomic studies. Six different methods for DNA extraction, encompassing two different commercial kits and three different protocols, were applied to material, so-called bio-swarf, from contemporary and archived jaws and vertebrae of tiger sharks (Galeocerdo cuvier). Protocols were compared for DNA yield and quality using a qPCR approach. For jaw swarf, all methods provided relatively high DNA yield and quality, while large differences in yield between protocols were observed for vertebrae. Similar results were obtained from samples of white shark (Carcharodon carcharias). Application of the optimized methods to 38 museum and private angler trophy specimens dating back to 1912 yielded sufficient DNA for downstream genomic analysis for 68% of the samples. No clear relationships between age of samples, DNA quality and quantity were observed, likely reflecting different preparation and storage methods for the trophies. Trial sequencing of DNA capture genomic libraries using 20000 baits revealed that a significant proportion of captured sequences were derived from tiger sharks. This study demonstrates that archived shark jaws and vertebrae are potential high-yield sources of DNA for genomic-scale analysis. It also highlights that even for similar tissue types, a careful evaluation of extraction protocols can vastly improve DNA yield.


PubMed | University of Queensland and Pepperell Research and Consulting Pty Ltd
Type: Journal Article | Journal: PloS one | Year: 2015

Increasing fishing pressure and uncertainty surrounding recreational fishing catch and effort data promoted the development of alternative methods for conducting fisheries research. A pilot investigation was undertaken to engage the Australian game fishing community and promote the non-lethal collection of tissue samples from the black marlin Istiompax indica, a valuable recreational-only species in Australian waters, for the purpose of future genetic research. Recruitment of recreational anglers was achieved by publicizing the project in magazines, local newspapers, social media, blogs, websites and direct communication workshops at game fishing tournaments. The Game Fishing Association of Australia and the Queensland Game Fishing Association were also engaged to advertise the project and recruit participants with a focus on those anglers already involved in the tag-and-release of marlin. Participants of the program took small tissue samples using non-lethal methods which were stored for future genetic analysis. The program resulted in 165 samples from 49 participants across the known distribution of I. indica within Australian waters which was a sufficient number to facilitate a downstream population genetic analysis. The project demonstrated the potential for the development of citizen science sampling programs to collect tissue samples using non-lethal methods in order to achieve targeted research objects in recreationally caught species.

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