Tag Archives: Papers

Paper submitted to Axios Review

A few months ago, my colleagues and I submitted to Fish and Fisheries a manuscript on the trade-offs between complexity and accuracy in random-effects models of body growth.

The paper was rejected mostly on the basis of lack of fit (i.e. the topic was only marginally interesting for the journal's readership). One Reviewer found the paper interesting and valuable, and recommended the submission of the manuscript to a more general journal, such as Ecology or Oikos. The other Reviewer commented on some unclear technical aspects of the work (the review was quite detailed and the recommendations/suggestions/critiques were valuable, thanks anonymous Reviewer).

I believe the paper should be of interest for a large audience of biologists, ecologists, computational scientists/statisticians. The main motivation of the paper is quite simple and very general: "We often face trade-offs between model complexity, biological interpretability of parameters, and goodness of fit." Then, with reference to models of growth: "Depending on formulation, parameters of some growth models may or may not be biologically interpretable. For instance the parameters of the widely used von Bertalanffy growth function (von Bertalanffy 1957) to model growth of fish may be considered either curve fitting parameters with no biological interpretation (i.e. providing phenomenological description of growth) or parameters that describe how anabolic and catabolic processes govern the growth of the organism (i.e. mechanistic description); see Mangel (2006). The classic von Bertalanffy growth function has 3 parameters: asymptotic size, growth coefficient, and theoretical age at which size is equal to 0. In the original mechanistic formulation of von Bertalanffy, asymptotic size results from the relationship between environmental conditions and behavioral traits and the growth coefficient is closely related to metabolic rates and behavioral traits (i.e. the same physiological processes affects both growth and asymptotic size). However, in the literature asymptotic size and growth rate are commonly treated as independent parameters with no connection to physiological functions, thus offering just a phenomenological description of growth."

However, I understand Editors may not fully grasp the relevance of the paper for their journal. For instance, the manuscript was previously submitted to another journal, but the Editor wrote: "I feel that the work is too specialised, as relatively few researcher work on growth curves". I might disagree on the claim that few researchers work on growth curves. I am sure that lots of scientists use growth models in their work, but I might agree on the number of people working on the development of growth models or methods for the estimation of growth model parameters (it is also quite hard).

My colleagues and I (my idea, my colleagues agreed) decided to submit the manuscript to Axios Review, a new service that should help authors publish their papers in higher profile journals. This is how it works: "Axios Review solves this problem by putting papers through rigorous external peer review and then referring them to the appropriate journal. When a journal asks the authors to revise and submit, the journal has effectively said that: i) the paper is within their scope, ii) that it is not fatally flawed, and iii) that it could be published in their journal. The Axios Review process effectively eliminates rejections on the grounds of novelty and significantly reduces the chances of rejection on quality. It’s similar to getting a ‘reject, encourage resubmission’ decision from the journal itself; for comparison, about 75% of resubmissions to top tier evolution journals get accepted. Authors submitting to Axios Review can have the reviewers comment on the suitability of their paper for any journal they choose, allowing them to aim for a high profile journal without the effort of formally submitting."

I submitted the manuscript to Axios Review a couple of days ago (target journals following an order that may or may not be the one I chose: Oikos, Ecology, Journal of Theoretical Biology, Ecological Applications). So far, communication with the Editorial staff has been excellent.

I did not upload the manuscript on arxiv or bioRxiv (I don't know where the manuscript will end up and thus which policy related to uploading of pre-print should I follow), please send an email if you'd like to read a pre-print.

 

Paper accepted in Marine Ecology Progress Series

Here below is the abstract.

Vincenzi S, Mangel M (accepted) Food abundance, kittiwake life histories, and colony dynamics in the Northeastern Pacific: implications of climate change and regime shifts. Marine Ecology Progress Series

Abstract

Black-legged kittiwakes Rissa tridactyla in the Northeastern Pacific will increasingly experience climate-induced changes in the variability of forage fish, which will influence both quantity and quality of food and may thus alter the population dynamics of kittiwake colonies. However, the relative roles of individual- and population-level traits in determining colony dynamics and risk of extinction are still unclear.

We combined models of components of the Pacific kittiwake life history with empirical data linking physiological stress and food abundance to provide a unified treatment of kittiwake colony dynamics. We simulated the dynamics of colonies with high, medium and low responsiveness of productivity to variation in nutritional stress in breeding birds, using data from Alaskan colonies. We found that the risk of quasi-extinction strongly decreased with a moderate increase of the potential number of yearly immigrants. Pre-breeding mortality as a function of growth during development had only a marginal role in determining median number of breeding pairs over simulation time. We predict that temporal auto-correlation of colony-wide average productivity and high nutritional stress, particularly if consistent over time, will increase quasi-extinction risk. Our work shows that colonies with low productivity have little chance to persist even when survival of pre-breeding and breeding birds is high, and that the nature of the temporal auto-correlation of food conditions and productivity is crucial to understand the effect of environmental fluctuations, regime shifts, and climate change on population dynamics of kittiwakes. We use the model to highlight the most valuable future empirical studies.

Papers I am "reading"

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When there is no volume/pages, it means it is in press ("in press" apparently still not supported by Mendeley)

Bateson, P., and K. N. Laland. 2013. Tinbergen’s four questions: an appreciation and an update. Trends in Ecology & Evolution.

Benyshek, D. C. 2013. The “early life” origins of obesity-related health disorders: New discoveries regarding the intergenerational transmission of developmentally programmed traits in the global cardiometabolic health crisis. American Journal of Physical Anthropology.

Berg, O. K., G. Bremset, M. Puffer, and K. Hanssen. 2013. Selective segregation in intraspecific competition between juvenile Atlantic salmon ( Salmo salar ) and brown trout (Salmo trutta). Ecology of Freshwater Fish.

Christiansen, F., G. a. Víkingsson, M. H. Rasmussen, and D. Lusseau. 2013. Female body condition affects foetal growth in a capital breeding mysticete. Functional Ecology.

Correia, D. 2013. F**k Jared Diamond. Capitalism Nature Socialism.

Ellegren, H. 2013. Genome sequencing and population genomics in non-model organisms. Trends in Ecology & Evolution.

Emery Thompson, M. 2013. Comparative Reproductive Energetics of Human and Nonhuman Primates. Annual Review of Anthropology 42:287–304.

French, W. E., B. Vondracek, L. C. Ferrington, J. C. Finlay, and D. J. Dieterman. 2013. Winter feeding, growth and condition of brown trout Salmo trutta in a groundwater-dominated stream. Journal of Freshwater Ecology 1–14.

Goto, A., H. Arioka, and R. Yokoyama. 2013. Plastic life-history variation along the course of a steep mountainous river in male Cottus hangiongensis (Pisces: Cottidae). Environmental Biology of Fishes.

Lanfear, R., H. Kokko, and A. Eyre-Walker. 2013. Population size and the rate of evolution. Trends in Ecology & Evolution.

Marcil-Ferland, D., M. Festa-Bianchet, A. M. Martin, and F. Pelletier. 2013. Despite Catch-Up, Prolonged Growth Has Detrimental Fitness Consequences in a Long-Lived Vertebrate. The American Naturalist .

Marks, J. 2013. The Nature/Culture of Genetic Facts*. Annual Review of Anthropology 42:247–267.

Moorad, J. A. 2013. Individual fitness and phenotypic selection in age-structured populations with constant growth rates List. Ecology.

Nelson, R. M., M. E. Pettersson, and O. Carlborg. 2013. A century after Fisher: time for a new paradigm in quantitative genetics. Trends in Genetics.

Robinson, O. J., N. H. Fefferman, and J. L. Lockwood. 2013. How to effectively manage invasive predators to protect their native prey. Biological Conservation 165:146–153.

Skolnick, A. M. H., A. Moroni, E. Siri, and L. Soliani. 1973. A Reconstruction of Historical Persons from the Parish Registers of Parma Valley , Italy. Genus 29:103–155. (related to a project I am working on and I will describe at some point)

Stier, A., V. a. Viblanc, S. Massemin-Challet, Y. Handrich, S. Zahn, E. R. Rojas, C. Saraux, et al. 2013. Starting with a handicap: phenotypic differences between early- and late-born king penguin chicks and their survival correlates. Functional Ecology.

 

Answering to reviewers

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How to answer to reviewers' points, suggestions, comments, rants etc. is something I consider every time I have to answer to reviewers, points, suggestions, comments, and especially rants. The Italian school, as far as I know, is on the very polite side of the fence. You start by writing:

We thank the Editor, Associate Editor, reviewers for the very interesting points, comments and suggestions (not rants) that will surely improve the new version of the manuscript. We are grateful for the possibility of resubmitting the paper (actually we would have preferred a major revision, but apparently the way of the Tao in the last 5 years is rejecting everything and then with some benevolence allowing a resubmission, which is not a guarantee of future consideration and absolutely not of future publication, since as stated in the bottom of the mail coming from the Editor, just before the signature, only 10 to 20% of the submitted manuscripts are getting published in this very selective journal because even in 2013 there is competition for space) and we answered in detail to each and every question, comment, suggestion, point raised by Editor, Associate Editor and reviewers. Thanks a lot again".

Then, in the actual "Response to Reviewers" you start the answers to reviewers' points (90% of the time), with "We perfectly agree with the reviewers" or "We understand reviewer's concern". Which, by the way, is true most of the time. When it is not true you write it anyway because looking for battles when they allowed you out of benevolence to submit a greatly revised version of the manuscript (because the previous one was totally unacceptable and also the Editor agreed with the reviewers) is not the way forward.

Now, how do I like authors to answer to my points when I am reviewing their papers? Do I care about how they answer (dear reviewer, thanks for your brilliant consideration) or only to what they answer (i.e. content)? Well, I'd say that I am much more interested in what they answer with respect to how they answer if how they answer is acceptable. I am very elastic and so far I never had any concerns. I am much more interested in science than in formalism. So, why am I paying more attention than other scientists (given my experience) on how I answer? Does it make a difference? It should not, but.

New paper submitted

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I submitted a new paper (aka tour de force) with title "Determining individual variation in growth and its implication for life history and population processes using the Empirical Bayes method" that is the result of a collaboration between myself, Marc Mangel, Hans Skaug, Steve Munch and Alain Crivelli. Four nations (Italy, US, Norway and France), multiple projects, one paper.

Here is the 200-word abstract:

The differences in demographic and life-history processes between organisms living in the same population have important consequences for ecological and evolutionary dynamics. Modern statistical and computational methods allow the investigation of individual and shared (among homogeneous groups) determinants of the observed variation.

We use an Empirical Bayes approach to estimate individual and shared variation in somatic growth with a random-effects model. As a case study, we consider two populations of marble trout Salmo marmoratus living in Slovenian streams, where individually‑tagged fish have been sampled for more than 15 years. We introduce cohort and density during the first year of life as potential predictors of the von Bertalanffy growth function’s parameters k and in addition to the individual random effects.

Our results showed that size ranks were largely maintained throughout lifetime in both populations. The best models according to the Akaike Information Criterion showed different growth patterns for year of birth cohorts as well as the existence of substantial individual variation in growth trajectories after accounting for the cohort effect. Model predictions of individual growth trajectories were largely more accurate than predictions based on mean size-at-age of fish. We consider both the life history origins of these patterns and their implications.

You can find data, code and a preprint on figshare. To run the code you need to install ADMB (I used version 11) and R. I think the total line of codes are between 5 and 10 thousand. It has been a long work (aka tour de force) and not-soon-to-be repeated.