Monday, September 7, 2015

Ben Pitcher with a cake for Pitcher et al. 2015: Chemical fingerprints reveal clues to identity, heterozygosity, and relatedness.

Here's Ben Pitcher presenting a cake for a new paper in PNAS entitled "Chemical fingerprints reveal clues to identity, heterozygosity, and relatedness", by Benjamin J. Pitcher, Isabelle Charrier, and Robert G. Harcourt.  


Olfaction is a key sense for mammals, and as a result chemical signals are an important means of communication for most mammalian species. It has long been established that most mammals make, distribute, and respond to chemosignals in a range of contexts, including reproduction, parent–offspring interactions, and social relationships (1). However, most aquatic mammals are unable to use olfaction when foraging, and evidence for its role in social behavior has been equivocal. Historically, reports in the literature have ranged from describing the semiaquatic pinnipeds as microsmatic (2) to those that have observed the high prevalence of naso-nasal inspection during social interactions (Fig. 1), and so inferred an important role for olfactory recognition (3). It is only recently that we experimentally confirmed in wild Australian sea lions that olfactory cues are a reliable mechanism in offspring recognition even in the absence of other sensory cues (4). Similarly, new experimental evidence in other large, wild mammals indicates the importance of olfactory cues in discrimination of potential mates and competitors as well as kin (5–7). However, perhaps due to both the complexity of working with natural vertebrate populations and the complexity of vertebrate scents, the mechanistic basis of chemical communication has received little study (8). In PNAS, Stoffel et al. (9) provide an important advance in the understanding of chemical communication in wild mammals. They compared genetic similarity and the chemical profiles of Antarctic fur seals in two colonies. In so doing they revealed that individual-specific chemical fingerprints have both inherited and environmental components and seem to encode mother–offspring similarity, heterozygosity, and genetic relatedness. The implications of these findings for chemical communication in wild mammals are profound.

Rob Harcourt with Adriano Zumbo cakes for Hussey et al. 2015, Aquatic animal telemetry: A panoramic window into the underwater world

Rob Harcourt presenting two fantastic Adriano Zumbo cakes in celebration of Hussey, N.E., Kessel, S.T., Aarestrup, K., Cooke, S.J., Cowley, P.D. Fisk, A.T., Harcourt, R.G., Holland, K.N., Iverson, S.J., Kocik, J.F., Mills Flemming, J.E., Whoriskey, F.G. 2015. Aquatic animal telemetry: A panoramic window into the underwater world. Science 1255642 (2015). DOI: 10.1126/science.1255642


A brave new world with a wider view

Researchers have long attempted to follow animals as they move through their environment. Until relatively recently, however, such efforts were limited to short distances and times in species large enough to carry large batteries and transmitters. New technologies have opened up new frontiers in animal tracking remote data collection. Hussey et al. review the unique directions such efforts have taken for marine systems, while Kays et al. review recent advances for terrestrial species. We have entered a new era of animal ecology, where animals act as both subjects and samplers of their environments.

Dan Warren with donuts for Mainali et al. 2015

Dan bringing some donuts for a new paper out in Global Change Biology: Projecting future expansion of invasive species: Comparing and improving methodologies for species distribution modeling, by Kumar P Mainali, Dan L Warren, Kunjithapatham Dhileepan, Andrew McConnachie, Lorraine Strathie, Gul Hassan, Debendra Karki, Bharat B Shrestha, and Camille Parmesan.

Here's the abstract:

Modeling the distributions of species, especially of invasive species in non-native ranges,
involves multiple challenges. Here, we developed some novel approaches to species
distribution modeling aimed at reducing the influences of such challenges and improving the
realism of projections. We estimated species-environment relationships with four modeling
methods run with multiple scenarios of (1) sources of occurrences and geographically
isolated background ranges for absences, (2) approaches to drawing background (absence)
points, and (3) alternate sets of predictor variables. We further tested various quantitative
metrics of model evaluation against biological insight. Model projections were very sensitive
to the choice of training dataset. Model accuracy was much improved by using a global
dataset for model training, rather than restricting data input to the species’ native range. AUC
score was a poor metric for model evaluation and, if used alone, was not a useful criterion for
assessing model performance. Projections away from the sampled space (i.e. into areas of
potential future invasion) were very different depending on the modeling methods used,
raising questions about the reliability of ensemble projections. Generalized linear models
gave very unrealistic projections far away from the training region. Models that efficiently fit
the dominant pattern, but exclude highly local patterns in the dataset and capture interactions
as they appear in data (e.g. boosted regression trees), improved generalization of the models.
Biological knowledge of the species and its distribution was important in refining choices
about the best set of projections. A post-hoc test conducted on a new Partenium dataset from
Nepal validated excellent predictive performance of our “best” model. We showed that vast
stretches of currently uninvaded geographic areas on multiple continents harbor highly
suitable habitats for Parthenium hysterophorus L. (Asteraceae; parthenium). However,
discrepancies between model predictions and parthenium invasion in Australia indicate
successful management for this globally significant weed.

Sunday, August 23, 2015

The Academic Cakewalk gauntlet has been thrown down

Tribolium cake, by Frances Jacomb.  This one was posted to the Academic Cakewalk Facebook group by Catherine Young.  The cake was made by Frances Jacomb to celebrate the end of data collection on a project on tribolium that Frances is doing with Luke Holman.  

Obviously this takes it to a whole new level, and everyone else is going to have to step up their game!

Thursday, June 4, 2015

Meeuwig et al. 2015 "When science places threatened species at risk "

This cake is for Meeuwig et al. 2015, entitled "When science places threatened species at risk".  The cake is presented by Rob Harcourt.

Short description:

The new information derived from telemetry combined with other biological knowledge suggests that shark-human interactions are largely random and rare events as sharks move through their habitats. Kill orders such as the one in WA are short-sighted, misdirected, target a political rather than an actual need, and block investment in knowledge generation. There is a serious need to ensure that science done through the tagging and tracking of animals is not used to generate contrary and morally questionable outcomes, particularly for threatened species. Ultimately, we improve ocean safety through enhanced knowledge rather than undermining the very basis of that knowledge by killing tagged research animals. 

Frère et al. 2015 "Polyandry in dragon lizards: inbred paternal genotypes sire fewer offspring"

This cake is to celebrate Frère et al. 2015, "Polyandry in dragon lizards: inbred paternal genotypes sire fewer offspring".  The cake (muffins) is presented by Martin Whiting.


Multiple mating in female animals is something of a paradox because it can either be risky (e.g., higher probability of disease transmission, social costs) or provide substantial fitness benefits (e.g., genetic bet hedging whereby the likelihood of reproductive failure is lowered). The genetic relatedness of parental units, particularly in lizards, has rarely been studied in the wild. Here, we examined levels of multiple paternity in Australia's largest agamid lizard, the eastern water dragon (Intellagama lesueurii), and determined whether male reproductive success is best explained by its heterozygosity coefficient or the extent to which it is related to the mother. Female polyandry was the norm: 2/22 clutches (9.2%) were sired by three or more fathers, 17/22 (77.2%) were sired by two fathers, and only 3/22 (13.6%) clutches were sired by one father. Moreover, we reconstructed the paternal genotypes for 18 known mother–offspring clutches and found no evidence that females were favoring less related males or that less related males had higher fitness. However, males with greater heterozygosity sired more offspring. While the postcopulatory mechanisms underlying this pattern are not understood, female water dragons likely represent another example of reproduction through cryptic means (sperm selection/sperm competition) in a lizard, and through which they may ameliorate the effects of male-driven precopulatory sexual selection.

Barneche and Allen 2015, Embracing general theory and taxon-level idiosyncrasies to explain nutrient recycling

This cake is to celebrate a paper by Barneche and Allen, entitled "Embracing general theory and taxon-level idiosyncrasies to explain nutrient recycling".  It is being presented by Diego Barneche.

Short description:

The value of mathematical theory in ecology is controversial; most ecologists are found in either side of a dichotomy: while some argue that general theory is the optimal way to advance mechanistic understanding in the discipline, others claim that general simple theory does not capture most of the variation in living systems. In our recent commentary piece (Barneche & Allen 2015), we argue that ecologists should embrace both views, and that this duality can be reconciled by using a combination of general mathematical theory and advanced statistical techniques, following a sequence of steps described below. These steps are exemplified using a recent study that uses a combination of predictions from the metabolic theory (MT) and ecological stoichiometry (ES) to explain body mass scaling of nutrient recycling rates in marine animals (Allgeier et al. 2015).

The first step entails recognising the scope of a given theory and explicitly declaring what assumptions are necessary to reach a given set of predictions. Allgeier et al. (2015) show that nutrient recycling rates follow 3/4-power body mass scaling, as should be predicted from MT-ES. Our study provides the theoretical rationale and the assumptions necessary to yield such prediction. In our view, this framework is essential to the understanding of ecological processes because false predictions serve as indications that one or more assumptions are violated/wrong – thus providing avenues on how to move forward on the understanding of ecological processes, either by modifying existing theory or by developing a new one. Although this assumption-prediction-testing-falsify cycle is the very core of the scientific method, it has been largely neglected in ecology.

The second step involves using statistical methods such as mixed effects models, which allow for the estimation of overall (i.e. mean) trends while accounting for deviations attributable to other variables not included in the theory. Many recent studies have made use of these mixed models to test for general theory while accounting for differences attributable to taxonomy (i.e. random effects) – there is to recognise that taxa might deviate from each other and from the overall trend. While taxonomy is not a true predictor in the sense that it characterises a process, it provides clues to what traits are responsible for differences among taxa, thus providing ideas on to how we should move forward.

The third and final step requires a careful exploration of how much variation is explained by different predictors, and what are the magnitudes of each one of them. For example, Allgeier et al. (2015) provides compelling evidence that despite substantial taxon-level idiosyncrasies (characterised as random effects in their LMM), body size is still the strongest predictor of nutrient recycling rates in marine animals. In our commentary, we notice that body size spans many orders of magnitude, while the other fixed-effect predictor (nutrient body content) spans less than one order of magnitude. However, the effect of body nutrient is stronger than that of body size, indicating that, for example, a doubling in body nutrient content has a greater effect in nutrient recycling rates than an equivalent increase in body mass.

We hope that with this roadmap, ecologists will increasingly embrace general theory and ecological idiosyncrasies in one single framework, which should help advance our understanding of ecological patterns and processes.

Wednesday, May 27, 2015

Vermeulen et al. 2015 "Investigation into potential transmission sources of Giardia duodenalis in a threatened marsupial (Petrogale penicillata)"

This cake is to celebrate a paper by Vermeulen et al., entitled  "Investigation into potential transmission sources of Giardia duodenalis in a threatened marsupial (Petrogale penicillata)".  It is being presented by Elke Vermeulen.


Assemblages of the protozoan parasite Giardia duodenalis common in humans and domestic species are increasingly identified in wildlife species, raising concern about the spill-over of pathogens from humans and domestic animals into wildlife. Here, the identity and prevalence of G. duodenalis in populations of a threatened marsupial, the brush-tailed rock-wallaby (Petrogale penicillata), was investigated. Identification of G. duodenalis isolates, across three loci (18S rRNA, β-giardin and gdh), from rock-wallaby fecal samples (n = 318) identified an overall detection rate of 6.3%. No significant difference in G. duodenalis detection was found among captive, wild and supplemented populations. Isolates were assigned to the zoonotic assemblages A and B at 18S rRNA, with sub-assemblages AI and BIV identified at the β-giardin and gdhloci, respectively. Assemblages AI and BIV have previously been identified in human clinical cases, but also in domestic animals and wildlife. The identification of these assemblages in brush-tailed rock-wallabies suggests there are transmission routes of G. duodenalis from humans or other animals to Australian wildlife, both in captivity and in the wild.

Wednesday, May 20, 2015

Chao et al. "Rarefaction and extrapolation of phylogenetic diversity"

This cake is to celebrate a paper by Chao et al., entitled "Rarefaction and extrapolation of phylogenetic diversity".  It's being presented by David Nipperess.

Short description:

1. Traditional species diversity measures do not make distinctions among species. Faith's phylogenetic diversity (PD), which is defined as the sum of the branch lengths of a phylogenetic tree connecting all species, takes into account phylogenetic differences among species and has found many applications in various research fields. In this paper, we extend Faith's PD to represent the total length of a phylogenetic tree from any fixed point on its main trunk.
2. Like species richness, Faith's PD tends to be an increasing function of sampling effort and thus tends to increase with sample completeness. We develop in this paper the ‘PD accumulation curve’ (an extension of the species accumulation curve) to depict how PD increases with sampling size and sample completeness.
3. To make fair comparisons of Faith's PD among several assemblages based on sampling data from each assemblage, we derive both theoretical formulae and analytic estimators for seamless rarefaction (interpolation) and extrapolation (prediction). We develop a lower bound of the undetected PD for an incomplete sample to guide the extrapolation; the PD estimator for an extrapolated sample is generally reliable up to twice the size of the empirical sample.
4. We propose an integrated curve that smoothly links rarefaction and extrapolation to standardize samples on the basis of sample size or sample completeness. A bootstrap method is used to obtain the unconditional variances of PD estimators and to construct the confidence interval of the expected PD for a fixed sample size or fixed degree of sample completeness. This facilitates comparison of multiple assemblages of both rarefied and extrapolated samples.
5. We illustrate our formulae and estimators using empirical data sets from Australian birds in two sites. We discuss the extension of our approach to the case of multiple incidence data and to incorporate species abundances.

A fortuitous collaboration that came out of an Ecological Statistics Symposium held at the University of New South Wales in July 2013. The paper is published in a special issue (New opportunities at the interface between ecology and statistics) dedicated to this particular symposium.

Tuesday, May 19, 2015

Momigliano et al. "Conserving coral reef organisms that lack larval dispersal:are networks of Marine Protected Areas good enough?"

This cake is to celebrate a paper by Momigliano et al., entitled "Conserving coral reef organisms that lack larval dispersal:are networks of Marine Protected Areas good enough?"  It's being present by Paolo Momigliano at Macquarie University.

Short description (no abstract since it's a perspective paper):

Coral reef ecosystems are under increasing threat due to the synergistic effects of habitat destruction, overfishing, eutrophication and climate change (Hughes et al., 2003, 2007; Hoegh-Guldberg et al., 2007). In response to these threats, management strategies that implement networks of Marine Protected Areas (MPAs) have gained momentum in the past few decades. Networks of MPAs can protect coral reef biodiversity from anthropogenic impacts either by eliminating the impacts of overfishing and habitat destruction, or by increasing ecosystem resilience to other anthropogenic disturbances (Russ and Zeller, 2003; McCook et al., 2010).

For networks of MPAs to be effective they must meet three key elements. Individual MPAs must be (1) partially self-seeding (Almany et al., 2007, 2009), (2) adequately connected to other MPAs via dispersal (Jones et al., 2007; Almany et al., 2009), and (3) they must protect target organisms during life stages when they are most vulnerable to anthropogenic impact (Zeller and Russ, 1998). Accordingly, MPAs should be large enough to encompass individual home ranges of the target species and to ensure a portion of the larvae produced within a MPA settles within its boundaries (Almany et al., 2009). Furthermore, networks of MPAs must ensure genetic and demographic connectivity between protected areas. Connectivity is defined as the exchange of individuals between populations. Connectivity bolsters local resilience to stochastic demographic fluctuations and in so doing, minimizes genetic erosion, the risk of inbreeding depression and ultimately maximizes adaptive potential (Almany et al., 2009).

Here we discuss how different life history strategies may affect the feasibility of achieving the three requirements for effective long-term conservation (self-seeding, connectivity, and protection). While sedentary organisms with a pelagic larval phase (most reef fishes and invertebrates), readily achieve this trinity (Planes et al., 2009), animals where dispersal only occurs as adults inevitably fail to meet all three requirements simultaneously (Figure 1). Here we propose a potential solution focusing on incorporating information on how habitat shapes adult dispersal to increase connectivity within networks of MPAs.

Iglesias et al. 2015, "Life in the unthinking depths: energetic constraints on encephalization in marine fishes"

This cake is to celebrate a paper by Iglesias et al., entitled "Life in the unthinking depths: energetic constraints on encephalization in marine fishes".  The cake is being presented by two of the authors, Teresa Iglesias and Dan Warren

Here's the abstract:

Several hypotheses have been proposed to explain the limitation of brain size in vertebrates. Here, we test three hypotheses of brain size evolution using marine teleost fishes: the direct metabolic constraints hypothesis (DMCH), the expensive tissue hypothesis and the temperature-dependent hypothesis. Our analyses indicate that there is a robust positive correlation between encephalization and basal metabolic rate (BMR) that spans the full range of depths occupied by teleosts from the epipelagic (< 200 m), mesope- lagic (2001000 m) and bathypelagic (> 4000 m). Our results disentangle the effects of temperature and metabolic rate on teleost brain size evolution, supporting the DMCH. Our results agree with previous findings that teleost brain size decreases with depth; however, we also recover a negative corre- lation between trophic level and encephalization within the mesopelagic zone, a result that runs counter to the expectations of the expensive tissue hypothesis. We hypothesize that mesopelagic fishes at lower trophic levels may be investing more in neural tissue related to the detection of small prey items in a low-light environment. We recommend that comparative encephalization studies control for BMR in addition to controlling for body size and  phylogeny.

About Academic Cakewalk

This blog is an attempt to foster scientific community and communication, primarily via the production and consumption of cakes.  In a number of labs and departments around the world, it is a bit of a tradition that when someone gets a paper published or passes a major career milestone (new job, fellowship, etc.), they bake a cake to celebrate.  The cake is presented to their colleagues, often with a bit of a short discussion about the paper or award.  We're hoping to spread this tradition, and to use it to encourage communication between labs.  Discussion of papers and/or cakes is heartily encouraged!

If you would like your lab or department's cakewalks to appear here, please feel free to email one of us and we will either post your cakewalks for you, or create and account so you can post your own.  Posts should include:

Photo of presenter with cake
Names of presenters
Title of paper and link to paper on original publisher's website
Anything else you want to add