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