Category Archives: Publishing papers

New paper accepted for publication by PRSB

A new manuscript I wrote with my long-term colleagues Marc Mangel, Dusan Jesensek, Carlos Garza, and Alain Crivelli has just been accepted by the Proceedings of the Royal Society B.

This is the cover letter, in which I explain the high-level picture and some details of the analyses (it may help some junior scientists still struggling with cover letters, too much, too little, too many details or not enough etc.).

Cover letter

Santa Cruz, 09/26/2016

Dear Editor,

We are pleased to submit our manuscript “Genetic and life-history consequences of extreme climate events” to PRSB.

The climate change-induced increased frequency and intensity of extreme climate events is one the major threats to the persistence of species. However, when dealing with extreme events, finding the right model system, posing and testing tractable hypotheses on their demographic, genetic, and life-history consequences, and developing an overarching predictive framework is very challenging. First, climate extremes are rare events, and as a consequence most of the empirical studies on their effects have been opportunistic and anecdotal. Then, the demographic, genetic, and life-history effects of extreme climate events are not easily predictable or generalizable across species or habitats, especially when the investigations are not guided by ecological and evolutionary biology theory.

In this work, we test – to our knowledge for the first time - theoretical predictions on the demographic, genetic, and life-history effects of extreme climate events on two populations of a fish species. The two populations have been drastically reduced in size by flash floods that occurred in 2007 and 2009. We used a statistically sophisticated approach that included reconstruction of pedigrees using long-term tag-recapture data (1995 to 2014 from one population, 2006 to 2014 for the other) and genotypes of more than 1,800 unique fish. In particular, we tested for faster life histories, higher variance in reproductive success, and loss of genetic variation after the extreme climate events.

We are confident that our study significantly advances our understanding of the demographic, genetic, and life-history effects of extreme climate events on natural populations and would be of great interest to a broad audience of biologists.

And here below is the abstract (I will soon post the pdf in the Publications page of the website).

Abstract

Climate change is predicted to increase the frequency and intensity of extreme climate events. Tests on empirical data of theory-based predictions on the consequences of extreme climate events are thus necessary to understand the adaptive potential of species and the overarching risks associated with all aspects of climate change. We tested predictions on the genetic and life-history consequences of extreme climate events in two populations of marble trout Salmo marmoratus that have experienced severe demographic bottlenecks due to flash floods. We combined long-term field and genotyping data, and pedigree reconstruction in a theory-based framework. Our results show that after flash floods, reproduction occurred at a younger age in one population. In both populations, we found the highest reproductive variance in the first cohort born after the floods due to a combination of fewer parents and higher early survival of offspring. A small number of parents allowed for demographic recovery after the floods, but the genetic bottleneck further reduced genetic diversity in both populations. Our results also elucidate some of the mechanism responsible for a greater prevalence of faster life histories after the extreme event.

Further considerations (some self-congratulatory)

These are some thoughts that I shared with one of my colleagues via email before submitting a revised version of the manuscript.

"Brief thoughts. This paper is an example of interdisciplinary work. There is solid life-history theory, we built up from previous work thus giving the sense of solid foundations and a on-going narrative, some hard tests as envisioned by Platt (age at reproduction decreases or not after the floods), demography, classic genetics, and state-of-the-art pedigree reconstruction.

Let's hope it gets accepted as is and we can then congratulate ourselves on an excellent, original work I am very proud of."

Manuscript submitted

I recently submitted a new manuscript on vital rates and life histories in marble trout. Dense paper, lots of models, lots of results. Currently under review. Here below are the Title and Abstract.

Title

Within and among-population variation in vital rates and population dynamics in a variable environment --- Vincenzi, Mangel, Jesensek, Garza, Crivelli.

Abstract

Understanding the causes of within- and among-population differences in vital rates, life histories, and population dynamics is a central topic in ecology. In order to understand how within- and among-population variation emerge, we need long-term studies that include episodic events and contrasting environmental conditions, tag-recapture data for the estimation and characterization of individual and shared variation, and statistical models that can tease apart population-, shared-, and individual contribution to the observed variation.

We used long-term tag-recapture data and novel statistical and modeling techniques to investigate and estimate within- and among-population differences in vital rates, life histories and population dynamics of marble trout Salmo marmoratus, a narrow endemic freshwater salmonid. Only ten populations of pure marble trout still persist in Western Slovenian headwaters. Marble trout populations are also threatened by floods and landslides, which have already caused the extinction of two populations in recent years.

In particular, we estimated and determined causes of variation and trade-offs within- and among populations in growth, survival, and recruitment in response to variation in water temperature, density, sex, early conditions, and extreme events.

In all ten populations, we found that the effects of population density on traits were mostly limited to the early stages of life and that individual growth trajectories were established early in life. We found no clear effects of water temperature on survival and recruitment. Population density was variable over time in all populations, with flash floods and debris flows causing massive mortalities and threatening population persistence. Apart from flood events, variation in population density within streams was largely determined by variation in recruitment, with survival of older fish being relatively constant over time within populations, but substantially different among populations. A fast- to slow-continuum of life histories in marble trout populations seemed to emerge, with slow growth associated with higher survival at the population level, possibly determined by food conditions and age at maturity.

Our work provides unprecedented insight into the causes of variation in vital rates, life histories, and population dynamics in an endemic species that is teetering on the edge of extinction.

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.

 

New paper submitted

Leave a reply

My friend and colleague Andrea Piotti and I have just submitted a paper for the special issue of Plant Ecology concerning the impact of extreme events on plants. We focused on the evolution of serotiny in pines in the face of an increasing probability of occurrence  of fires with climate and anthropogenic change. Title and abstract below. Please ask me for a preprint if interested.

Evolution of serotiny in maritime pine (Pinus pinaster) in the light of increasing frequency of fires

Abstract

Wildfire frequency and intensity in the Mediterranean region is predicted to increase with climate and anthropogenic change in the following decades. Pines species often posses fire-embracing and fire-avoiding strategies that increase the probability of persistence and performance in fire-prone habitats.

One such strategy is serotiny, i.e. the capacity to retain seeds in long-closed cones within the plant canopy; serotinous cones release seeds only when either a fire or a heat shock occurs. In this work, we used a simulation approach and P. pinaster populations as a model system to investigate how (i) an increased frequency of fire, (ii) genetic characteristics of serotiny, and (iii) observed differences in life histories interact to determine: (a) risk of local population extinction and (b) temporal changes in the prevalence of serotiny in the modeled population. In addition, we tested whether the contemporary evolution of serotiny in the face of increased probability of occurrence of fires increased the probability of population persistence with respect to a scenario in which serotiny was not allowed to evolve. Our simulations showed that over the 300 years of simulated time the evolution of serotiny did not substantially contribute to the persistence of populations. Extinction risk increased with increasing probability of occurrence of fire and slightly decreased with (i) higher gene flow from outside the modelled population, and (ii) with higher prevalence of serotiny at the beginning of the simulation. The prevalence of serotiny at the end of simulation time was difficult to predict and mostly driven by stochasticity.

Keywords: Extreme events; gene flow; population dynamics; extinction risk, adaptation; climate change

Marie-Curie related paper accepted for publication

Leave a reply

Paper accepted by Journal of Fish Biology. Title, Authors, Abstract, Keywords here below. Code is here.

Eco-evolutionary dynamics induced by massive mortality events

Simone Vincenzi, Alain J Crivelli, William H Satterthwaite, Marc Mangel

Abstract: To explore the selective consequences of severe disturbance events, an eco-genetic model tuned on a population of marble trout Salmo marmoratus subject to periodic flood events was used to explore how the evolution of growth rates interacting with density-dependent processes can modify size-at-age and population structure, and in turn influence the resilience of populations. Fish with greater growth potential were assumed to have higher mortality rates. The results of simulations were compared between two scenarios, one in which populations may evolve growth rates and one in which the distribution of growth rates within a population is kept fixed. Evolving populations had greater proportion of age-1 individuals in the population, greater median length at age 3 (the typical age at sexual maturity for marble trout) and lower population sizes. The slightly smaller population sizes did not affect realized extinction risk. Resilience, defined as the number of years necessary to rebound from flood-induced population collapse, was on average from 2 to 3 years in both scenarios, with no significant difference between them.  Moderate heritability of growth, relaxation of density-dependent processes at low densities and rapid recovery to a safe population size all combine to limit the capacity to evolve faster recovery after flood-induced population collapses via changing growth rates.

Keywords: Somatic growth; marble trout; trade-off; life histories; floods.

Answering to reviewers

Leave a reply

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

Leave a reply

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.

NSF reviews and grade inflation

Leave a reply

I just completed a review for the NSF on a very interesting proposal in the ecological, population biology etc. area. Probably because I am foreign national, this is the first time (maybe the second and the first time I declined?) I was asked to provide a review. After completing my summary I had to choose the final grade. I thought Very Good was the right grade because they were a couple of things that needed to be addresses, but I remembered what John Boyd was saying about "grades" in the army, where being merely excellent meant not being suitable for promotion. "Colonel is excellent in every aspect" meant between the lines that the Colonel was getting sacked. You needed to be super or ultra excellent in every aspect and more. Boyd is an interesting read by the way, although apparently his influence in the military has been in the neighborhood of nothing ("folk hero" has been the definition of someone in the know). One time I also took inspiration from his analysis and synthesis dual approach to learning and understanding for my teaching statement in a job application, but apparently the committee thought I was merely excellent and not super excellent. Now that I remember (refresher here) Boyd was also very very weird, so maybe taking inspiration from his bizarre views was not a good strategy. Better in any case than being boring (remember than interesting is better than boring and fun is better than not fun, although right is most of the time better than wrong and this may create conflicts with the fun part) with all the "my mission in life is teaching undergrads and please give me a job and I will teach 4 courses each quarter (give me a job is the lynchpin, by the way)". So, I might propose again the analysis/synthesis destruction/creation dual approach, just for the fun of it (and I also believe it is an interesting approach, at least it was at the time). I will tell you how it goes. By the way, I enjoying teaching undergrads.

Getting back to grades, I googled online and I came across this 3 years old post from the popular Female Professor blog. After reading that Very Good is not actually very good, but, meh, kinda good, I bumped my grade to Excellent since I believe that the proposal should get funded. Be aware fellow reviewers that what you write should reflect what you think as well as what they think you are thinking. Since you do not know what they are thinking, bumping up might be generally a good strategy. At least, that was my choice.