CIE Spotlight: De novo genome assembly and annotation of Australia’s largest freshwater fish, the Murray cod (Maccullochella peelii), from Illumina and Nanopore sequencing read

AuthorsChristopher M. Austin, Mun Hua Tan, Katherine A. Harrisson, Yin Peng Lee, Laurence J. Croft, Paul Sunnucks, Alexandra PavlovaHan Ming Gan

Source: GigaScience: Volume 6, Issue 8, (2017).

Brief summary of the paper: One of the most iconic Australian fish is the Murray cod, Maccullochella peelii (Mitchell 1838), a freshwater species that can grow to ∼1.8 metres in length and live to age ≥48 years. The Murray cod is of a conservation concern as a result of strong population contractions, but it is also popular for recreational fishing and is of growing aquaculture interest.

In this study, we report the whole genome sequence of the Murray cod to support ongoing population genetics, conservation, and management research, as well as to better understand the evolutionary ecology and history of the species. A draft Murray cod genome of 633 Mbp (N50 = 109 974bp; BUSCO and CEGMA completeness of 94.2% and 91.9%, respectively) with an estimated 148 Mbp of putative repetitive sequences was assembled from the combined sequencing data of 2 fish individuals with an identical maternal lineage; 47.2 Gb of Illumina HiSeq data and 804 Mb of Nanopore data were generated from the first individual while 23.2 Gb of Illumina MiSeq data were generated from the second individual.

The inclusion of Nanopore reads for scaffolding followed by subsequent gap-closing using Illumina data led to a 29% reduction in the number of scaffolds and a 55% and 54% increase in the scaffold and contig N50, respectively. We also report the first transcriptome of Murray cod that was subsequently used to annotate the Murray cod genome, leading to the identification of 26 539 protein-coding genes. We present the whole genome of the Murray cod and anticipate this will be a catalyst for a range of genetic, genomic, and phylogenetic studies of the Murray cod and more generally other fish species of the Percichthydae family.

CIE Spotlight: Managing too little and too much water: Robust mine-water management strategies under variable climate and mine conditions

Authors: Lei Gao, Brett Bryan, Jian Liu, Wanggen Li, Yun Chen, Rui Liu, Damian Barrett

SourceJournal of Cleaner Production: 16:1009-1020, (2017).

Brief summary of the paper: Mine-water managers need tools to guide robust management strategies that can address the challenges of climate-influenced water scarcity and unregulated discharge. We aimed to identify those factors driving the risks of insufficient water supply for mine production and unpermitted discharge of mine-affected water in a way that is robust to heterogeneity between extreme climatic variability and mine sites.

Using 16 coal mines in the Bowen Basin of Queensland, Australia, as a case study, we combined a model of complex mine-water management systems (C-HSM) with global sensitivity analysis (eFAST) to identify influential mine-water management factors. Comprehensive model diagnostics for the 16 mine-water systems under three climate conditions revealed that the uncertainty of key mine-water management indicators, and the contributions of model input parameters differed substantially between climate conditions and mine sites. We then applied four criteria from decision theory into the total sensitivity effects produced by the eFAST method, and developed sensitivity indicators that were robust to heterogeneity between climates and mine sites.

These sensitivity indicators provide mine-water managers with options to guide the development of effective management strategies and the collection of additional information based on their own risk preference. While our results indicate some general management strategies that will be robust under multiple conditions, we caution that mine-water managers’ experience in dealing with challenges caused by too little and too much water cannot be blindly transplanted from one mine to another, or from one climate condition to another.

CIE Spotlight: Endocrine differences among colour morphs in a lizard with alternative behavioural strategies

Authors: Madeleine St Clair Yewers, Tim S. Jessop, Devi Stuart-Fox

SourceHormones and Behavior: Volume 93, July 2017, Pages 118-127

Brief summary of the paper:Alternative behavioural strategies of colour morphs are expected to associate with endocrine differences and to correspond to differences in physical performance (e.g. movement speed, bite force in lizards); yet the nature of correlated physiological and performance traits in colour polymorphic species varies widely. Colour morphs of male tawny dragon lizards Ctenophorus decresii have previously been found to differ in aggressive and anti-predator behaviours.

We tested whether known behavioural differences correspond to differences in circulating baseline and post-capture stress levels of androgen and corticosterone, as well as bite force (an indicator of aggressive performance) and field body temperature. Immediately after capture, the aggressive orange morph had higher circulating androgen than the grey morph or the yellow morph. Furthermore, the orange morph maintained high androgen following acute stress (30 min of capture); whereas androgen increased in the grey and yellow morphs. This may reflect the previously defined behavioural differences among morphs as the aggressive response of the yellow morph is conditional on the colour of the competitor and the grey morph shows consistently low aggression.

In contrast, all morphs showed an increase in corticosterone concentration after capture stress and morphs did not differ in levels of corticosterone stress magnitude (CSM). Morphs did not differ in sizeand temperature-corrected bite force but did in body temperature at capture. Differences in circulating androgen and body temperature are consistent with morph-specific behavioural strategies in C. decresii but our results indicate a complex relationship between hormones, behaviour, temperature and bite force within and between colour morphs.

CIE Spotlight: Resource availability and sexual size dimorphism: differential effects of prey abundance on the growth rates of tropical snakes

Authors: Gregory P. Brown, Thomas R. L. Madsen, Rick Shine

Source: Functional Ecology: 31:1592–1599, (2017).

Brief summary of the paper:

  1. Broad phylogenetic patterns in sexual size dimorphism (SSD) are shaped by sex differences in net selection pressures (e.g. sexual selection, fecundity selection, survival selection), but environmental and ecological factors can also affect the expression of SSD.
  2. Discussions of proximate ecological influences on SSD have focused on niche divergence; for example, increase in a prey type used by only one sex can elevate growth rates of that sex but not the other. Food limitation also can generate spatial and temporal variation in SSD. Under restricted prey abundance, curtailed growth may mask SSD even if the optimal size is greater for one sex than the other. Because an increase in food availability elicits increased feeding and growth by the sex that benefits more from increased body size, variation in prey abundance can generate variation in SSD.
  3. We used mark-recapture methods to study growth rates relative to prey (frog) abundance in two species of sexually dimorphic colubrid snake species in tropical Australia.
  4. In slatey-grey snakes (Stegonotus cucullatus), a species in which larger body size enhances reproductive output in both sexes (because larger males win combat bouts, and larger females produce more/heavier eggs), increased abundance of frogs caused equivalent increases in growth rates in both sexes and hence did not affect SSD. In keelbacks (Tropidonophis mairii), a species in which larger size enhances reproductive output in females more than males (reflecting a lack of male–male combat), increased abundance of frogs elicited higher growth rates of females only. Thus, SSD in keelbacks was modified by prey abundance.
  5. Our results show that the magnitude of sex differences in adult body size can be influenced by proximate environmental factors and support the hypothesis of sex-specific targets for maximum feeding rates.

CIE Spotlight: Popular media records reveal multi-decadal trends in recreational fishing catch rates

AuthorsRuth H. ThurstanEdward Game, John M. Pandolfi

Source: PLOS ONE: 12(8): e0182345, 2017.

Brief summary of the paper: Despite threats to human wellbeing from ecological degradation, public engagement with this issue remains at low levels. However, studies have shown that crafting messages to resonate with people’s personal experiences can enhance engagement. Recreational fishing is one of the principal ways in which people interact with aquatic environments, but long-term data from this perspective are considered rare.

We uncovered 852 popular media records of recreational fishing for an Australian estuary across a 140-year period. Using information contained in these articles we analysed the species composition of recreational catches over time and constructed two distinct time series of catch and effort (n fish fisher-1 trip-1; kg fish fisher-1 trip-1) for recreational fishing trips and fishing club competitions (mean n and kg fish caught across all competitors, and n and kg fish caught by the competition winner). Reported species composition remained similar over time. Catch rates reported from recreational fishing trips (1900–1998) displayed a significant decline, averaging 32.5 fish fisher-1 trip-1 prior to 1960, and 18.8 fish fisher-1 trip-1 post-1960. Mean n fish fisher-1 competition-1 (1913–1983) also significantly declined, but best n fish fisher-1 competition-1 (1925–1980) displayed no significant change, averaging 31.2 fish fisher-1 competition-1 over the time series. Mean and best kg fish fisher-1 competition-1 trends also displayed no significant change, averaging 4.2 and 9.9 kg fisher-1 competition-1, respectively.

These variable trends suggest that while some fishers experienced diminishing returns in this region over the last few decades, the most skilled inshore fishers were able to maintain their catch rates, highlighting the difficulties inherent in crafting conservation messages that will resonate with all sections of a community. Despite these challenges, this research demonstrates that popular media sources can provide multiple long-term trends at spatial scales, in units and via a recreational experience that many people can relate to.

CIE Spotlight: Aerial and underwater surveys reveal temporal variation in cleaning-station use by sea turtles at a temperate breeding area

AuthorsGail Schofield, Kostas Papafitsoros, Rebecca Haughey, Kostas Katselidis

Source: Marine Ecology Progress Series: 575:153-164 (2017)

Brief summary of the paper: Many animals invest time and energy in removing unwanted organisms from their body surface; however, the benefits of symbiotic cleaning associations to ‘clients’ are disputed. We used aerial (unmanned aerial vehicles, UAVs) and underwater surveys to investigate whether loggerhead sea turtles Caretta caretta actively or incidentally invested in using fish-cleaning stations at a temperate breeding area (Zakynthos, Greece), although they are expected to minimize movement to divert energy to egg development. If the former, we hypothesized that turtles would swim into the station (UAV surveys), visit multiple times and compete for access (underwater surveys).

Underwater surveys showed that station location changed annually, ruling out usage of a long-term cognitive memory. UAV surveys showed that turtles began using the station immediately after mating activity decreased (mid-May), with use remaining high until females departed (July). Wind direction (primarily southerly) was correlated with the frequency of use (UAV and underwater surveys) and direction of movement through the station (from upwind to downwind); however, turtles swam actively (i.e. did not simply drift).

Of the unique turtles photo-identified during underwater surveys, 25 and 18% of individuals were detected multiple times within and across surveys, respectively, with at least 2 turtles competing for access to cleaner fish in most surveys. UAV surveys showed that more turtles were present within 100 m of the station compared to the turtles detected by underwater surveys at the station, suggesting individuals may visit the station repeatedly through the day. We conclude that turtles might initially find a station incidentally; however, repeated visits and competition for access suggest that turtles receive direct (stress relief, epibiont removal) and/or indirect (health, fitness, migratory) benefits.

CIE Spotlight: Demographic consequences of fisheries interaction within a killer whale (Orcinus orca) population

AuthorsPaul TixierChristophe Barbraud, Deborah Pardo, Nicolas Gasco, Guy Duhamel, Christophe Guinet

Source: Marine Biology, 164:170 (2017).

Brief summary of the paperIndividual heterogeneity in foraging behavior has been widely documented within predator populations. In highly social apex predators such as killer whales (Orcinus orca), specialization may occur at the matriline level. A small population of killer whales has been documented to occur around the Crozet Islands. These whales feed on a wide range of prey items including seals, penguins and large whales, as well as depredate the local Patagonian toothfish (Dissostichus eleginoides) longline fishery. The level of interactions with fisheries varies greatly between matrilines.

Here, we present the results on the effects of such behavioral heterogeneity on the demographic trends of this killer whale population. We used photo-identification data from 1977 to 2011 in a mark–recapture framework to test the effect of varying levels of fisheries interactions on adult survival. We documented significant differences in survival between depredating and non-depredating whales, resulting in divergent intra-population demographic trends. These differences showed low survival, and thus a negative effect, for depredating whales when illegal fishing occurred (poachers used lethal methods to deter killer whales from depredating longlines).

After illegal fishing stopped (2003–2011), the survival rates of depredating individuals exceeded the survival rates of non-depredating individuals, suggesting a positive influence of “artificial food provisioning”. This effect was further supported by a higher population growth rate for depredating whales. This study highlights the potential demographic costs and benefits that cetaceans face from depredating fisheries and addresses the demographic consequences of both intra-population feeding specialization and the influence of anthropogenic changes in resource availability.

CIE Spotlight: Is behavioural plasticity consistent across different environmental gradients and through time?

Authors: David Mitchell, Peter Biro

Source: Proceedings of The Royal Society B: 10.1098/rspb.2017.0893

Brief summary of the paperDespite accumulating evidence for individual variation in behavioural plasticity, there is currently little understanding of the causes and consequences of this variation. An outstanding question is whether individual reaction norm (RN) slopes are consistent across different environmental variables—that is, whether an individual that is highly responsive to one environmental variable will be equally responsive to a second variable. Another important and related question is whether RNs are themselves consistently expressed through time or whether they are simply state dependent.

Here, we quantified individual activity rates of zebrafish in response to independent manipulations of temperature and food availability that were repeated in discrete ‘bursts’ of sampling through time. Individuals that were thermally responsive were not more responsive to food deprivation, but they did exhibit greater unexplained variation. Individual RN slopes were consistent (repeatable) over time for both temperature (Rslope = 0.92) and food deprivation responses (Rslope = 0.4), as were mean activity rates in the standard environment (Rintercept = 0.83). Despite the high potential lability of behaviour, we have demonstrated consistency of behavioural RN components and identified potential energetic constraints leading to high consistency of thermal RNs and low consistency of food deprivation RNs.

CIE Spotlight: Decision-Making in Conservation and Natural Resource Management: Models for Interdisciplinary Approaches

Edited by: Nils Bunnefeld, Emily Nicholson, EJ Milner-Gulland

Source: Conservation Biology (Cambridge University Press), Volume: 22, August 2017

Brief summary of the book: Making decisions about the management and conservation of nature is necessarily complex, with many competing pressures on natural systems, opportunities and benefits for different groups of people and a varying, uncertain social and ecological environment.

An approach which is narrowly focused on either human development or environmental protection cannot deliver sustainable solutions. Decision-Making in Conservation and Natural Resource Management provides frameworks for improving the integration of natural resource management with conservation and supporting stronger collaboration between researchers and practitioners in developed and developing countries.

Novel approaches are required when ecological and social dynamics are highly interdependent. A structured, participatory, model-based approach to decision-making for biodiversity conservation has been proven to produce real-world change. There are surprisingly few successful case studies, however; some of the best are presented here, from fisheries, pest management and conservation. Researchers and practitioners need this interdisciplinary approach, focused on quantitative tools that have been tested and applied, and learning from success.

CIE Spotlight: Changes in diet associated with cancer

Authors: Frédéric Thomas, Sophie Rome,Frédéric Mery, Erika Dawson, Jacques Montagne, Peter A. BiroChrista Beckmann, François Renaud, Robert Poulin, Michel Raymond and Beata Ujvari

Source: EVOLUTIONARY APPLICATIONS, 10:651–657, 2017 (Open Access)

Brief summary of the paperChanges in diet are frequently correlated with the occurrence and progression of malignant tumors (i.e., cancer) in both humans and other animals, but an integrated conceptual framework to interpret these changes still needs to be developed. Our aim is to provide a new perspective on dietary changes in tumor-bearing individuals by adapting concepts from parasitology.

Dietary changes may occur alongside tumor progression for several reasons: (i) as a pathological side effect with no adaptive value, (ii) as the result of self-medication by the host to eradicate the tumor and/or to slow down its progression, (iii) as a result of host manipulation by the tumor that benefits its progression, and finally (iv) as a host tolerance strategy, to alleviate and repair damages caused by tumor progression. Surprisingly, this tolerance strategy can be beneficial for the host even if diet changes are beneficial to tumor progression, provided that cancer-induced death occurs sufficiently late (i.e., when natural selection is weak).

We argue that more data and a unifying evolutionary framework, especially during the early stages of tumorigenesis, are needed to understand the links between changes in diet and tumor progression. We argue that a focus on dietary changes accompanying tumor progression can offer novel preventive and therapeutic strategies against cancer.