diff --git a/docs/AmNat_MS_template.tex b/docs/AmNat_MS_template.tex new file mode 100644 index 0000000..d95bd69 --- /dev/null +++ b/docs/AmNat_MS_template.tex @@ -0,0 +1,386 @@ +\documentclass[11pt]{scrartcl} +\usepackage[sc]{mathpazo} %Like Palatino with extensive math support +\usepackage{fullpage} +\usepackage[authoryear,sectionbib,sort]{natbib} +\linespread{1.7} +\usepackage[utf8]{inputenc} +\usepackage{lineno} +\usepackage{titlesec} +\titleformat{\section}[block]{\Large\bfseries\filcenter}{\thesection}{1em}{} +\titleformat{\subsection}[block]{\Large\itshape\filcenter}{\thesubsection}{1em}{} +\titleformat{\subsubsection}[block]{\large\itshape}{\thesubsubsection}{1em}{} +\titleformat{\paragraph}[runin]{\itshape}{\theparagraph}{1em}{}[. ]\renewcommand{\refname}{Literature Cited} + +%%%%%%%%%%%%%%%%%%%%% +% Line numbering +%%%%%%%%%%%%%%%%%%%%% +% +% Please use line numbering with your initial submission and +% subsequent revisions. After acceptance, please turn line numbering +% off by adding percent signs to the lines %\usepackage{lineno} and +% to %\linenumbers{} and %\modulolinenumbers[1] below. +% +% To avoid line numbering being thrown off around math environments, +% the math environments have to be wrapped using +% \begin{linenomath*} and \end{linenomath*} +% +% (Thanks to Vlastimil Krivan for pointing this out to us!) + +\title{Template and Guidelines for Using \LaTeX{} in \textit{The~American~Naturalist} } + +% This version of the LaTeX template was last updated on +% July 16, 2024. + +%%%%%%%%%%%%%%%%%%%%% +% Authorship +%%%%%%%%%%%%%%%%%%%%% +% Please commet out authorship information while your paper is under review. +% You will need to add this information back in to your final files after +% acceptance. + +\author{Owen E. Cook$^${1,\ast}$ \\ +Generic H. Collaborator$^{2,\dag}$ \\ +Additional Q. Expert$^{3}$} + +\date{} + +\begin{document} + +\maketitle + +\noindent{} 1. University of Chicago, Chicago, Illinois 60637; + +\noindent{} 2. University of Toronto, Toronto, Ontario M5S 1A5, Canada; + +\noindent{} 3. Middle Eastern Technical University, Çankaya, Ankara 06800, Turkey. + +\noindent{} $\ast$ Corresponding author; e-mail: amnat@uchicago.edu. + +\noindent{} $\dag$ Deceased. + +\bigskip + +\textit{Manuscript elements}: Figure~1, figure~2, table~1, appendix~A (for print; including figure~A1, figure~A2, and table~A1), supplemental PDF. Figure~2 is to print in color. + +\bigskip + +\textit{Keywords}: Examples, model, template, guidelines. + +\bigskip + +\textit{Manuscript type}: Article. %Or note, natural history miscellany note, comment, reply, invited symposium, featured topic, or historical perspective. + +\bigskip + +\noindent{\footnotesize Prepared using the suggested \LaTeX{} template for \textit{Am.\ Nat.}} + +\linenumbers{} +\modulolinenumbers[1] + +\newpage{} + +\section*{Abstract} + +Lorem ipsum dolor sit amet, consectetur adipiscing elit. Sed non risus. Suspendisse lectus tortor, dignissim sit amet, adipiscing nec, ultricies sed, dolor. Cras elementum ultrices diam. Praesent quis dolor in dolor molestie cursus et ac nisi. Vestibulum ante purus, semper eget est vitae, vehicula ornare nisl. Morbi efficitur euismod enim, nec feugiat tellus cursus eget. + +\newpage{} + +\section*{Introduction} + +% The journal does not have numbered sections in the main portion of +% articles. Please refrain from using section references (à la +% section~\ref{section:CountingOwlEggs}), and refer to sections by name +% (e.g. section ``Counting Owl Eggs''). + +The quick red fox jumps over the lazy brown dog. Furthermore, the quick brown fox jumps over the lazy red dog. In addition, the quick R\"{u}ppell's fox (\textit{Vulpes rueppellii}) jumps over the lazy golden retriever. + +\section*{Methods} + +Lorem ipsum ut velit mauris, egestas sed, gravida nec, ornare ut, mi. Aenean ut orci vel massa suscipit pulvinar. Nulla sollicitudin. Fusce varius, ligula non tempus aliquam, nunc turpis ullamcorper nibh, in tempus sapien eros vitae ligula (\citealt{OriginSpec}). + +\subsection*{Second-order heading} + +Lorem ipsum nulla facilisi, pace \citet{LemKapEx07}. Etiam semper, orci sit amet facilisis interdum, tellus nunc consequat erat, quis viverra nisi diam ut metus. Pellentesque cursus, sapien malesuada euismod iaculis, mauris purus interdum diam, vel vestibulum justo enim vitae tellus. Nunc interdum lorem sit amet diam volutpat tristique. Quisque pulvinar ac metus commodo lacinia (\citealt{Ing11,Xiao2015}). + +\subsubsection*{Third-order heading} + +Usually two or three levels of heading will be all you need. Journal style even permits a fourth level in case you need it. + +\paragraph*{Fourth-order heading} +The quick red fox jumps over the lazy brown dog in this paragraph as well. Donec mauris nibh, volutpat vehicula viverra at, iaculis congue sem. Praesent eget erat rhoncus erat sollicitudin volutpat. + +\begin{equation} +{ \frac{1}{N_k-1} \sum \limits_{t=1}^{N_k} (M_{tjk} - \bar{M}_{jk})^2} +\end{equation} + +Praesent quis dolor in dolor molestie cursus et ac nisi. Vestibulum ante purus, semper eget est vitae, vehicula ornare nisl. Morbi efficitur euismod enim, nec feugiat tellus cursus eget. Donec mauris nibh, volutpat vehicula viverra at, iaculis congue sem. + +\subsection*{Another second-order heading} + +As \citet{Xiao2015} argued, phasellus porttitor eros et ante condimentum, eget facilisis orci condimentum. Nulla facilisi. Proin placerat elit blandit, euismod dolor nec, dapibus diam. Mauris posuere malesuada lacus, at elementum lacus auctor eu (fig~\ref{Fig:Jumps}A). + +\section*{Results} + +Lorem ipsum dolor sit amet. Aenean pulvinar malesuada commodo (see \citealt{DavisEtAl2011}; table~\ref{Table:Founders}). Sed aliquet mauris odio, in tristique dui egestas a. Etiam eu malesuada quam. Suspendisse tincidunt eu erat sit amet vulputate. Duis at arcu et nisl dictum mattis. Maecenas vel cursus ante. Cras eleifend elit nec velit sollicitudin fermentum in ac mauris. Pellentesque rutrum magna vel elit maximus hendrerit. + +\subsection*{The height of the jump} + +Aenean eu pellentesque quam (fig.~\ref{Fig:OkapiHorn}). Nam pellentesque augue eu finibus lacinia. Nullam nec justo vitae odio imperdiet rhoncus vitae vitae quam. Pellentesque porttitor metus et lectus ornare, ac cursus urna efficitur (fig~\ref{Fig:Jumps}B). + +\subsection*{The laziness of the dog} + +Example paragraph with embedded references (video~\ref{VideoExample}, fig.~\ref{Fig:AnotherFigure}). +If you have deposited data to Dryad, it is advisable to cite them somewhere in the main text (usually in the Methods or Results sections). A sentence like the following will do: All data are available in the Dryad Digital Repository (\citealt{CookEtAl2015}). + +\section*{Discussion} + +Nam pulvinar lorem at lorem ultrices, vel accumsan massa feugiat (\citealt{Ing11}). Proin tristique velit eget lacus iaculis, in pellentesque nulla varius. Phasellus sodales est odio, eu pulvinar magna pellentesque eu. Sed ut lobortis eros. Aliquam eget metus turpis. Sed et convallis lectus, id tincidunt enim. In porta nibh ut lacus feugiat, non consequat orci rhoncus. Morbi blandit at augue nec tempor. Sed fringilla ipsum ut justo viverra, ut euismod nisi gravida. + +Curabitur non posuere augue, id suscipit orci. Nunc luctus accumsan aliquam. Cras egestas turpis vitae nisl vulputate interdum. Donec pellentesque libero egestas tortor pharetra laoreet. Phasellus facilisis auctor ligula, eu sollicitudin mi sagittis non. + +\section*{Conclusion} + +Duis pharetra enim at libero cursus, eu commodo mi vestibulum. Nullam eget velit nec lectus viverra sodales. Suspendisse egestas, eros at dictum tincidunt, mi orci laoreet libero, eget rutrum sapien arcu blandit odio. + +%%%%%%%%%%%%%%%%%%%%% +% Acknowledgments +%%%%%%%%%%%%%%%%%%%%% +% You may wish to remove the Acknowledgments section while your paper +% is under review as the Acknowledgments may reveal your identity. +% If you remove this section, you will need to add it back in to your +% final files after acceptance. + +\section*{Acknowledgments} + +OEC would like to thank Madlen Wilmes, Gyuri Barab\'{a}s, Flo D\'{e}barre, Vlastimil K\v{r}ivan, and Greg Dwyer for their comments and suggestions on this template. + +%%%%%%%%%%%%%%%%%%%%% +% Statement of Authorship +%%%%%%%%%%%%%%%%%%%%% +% This section should also be commented out while your MS is undergoing +% double-blind review. The specifics should of course be adapted to +% your paper, but the paragraph below gives some hints of possible +% contributions. + +\section*{Statement of Authorship} + +OEC conceived the experiments, collected the data, and wrote the original draft. +GHC provided specimens and analyzed the model. +AQE oversaw data analysis and developed the code. +All authors reviewed and edited the writing at all stages of revision. + +\section*{Data and Code Availability} + +On initial submission, you may use this section to provide a URL for editors and reviewers that is `private for peer review'. After acceptance, this section must be updated with correct, working DOIs for data and code deposits (such as in Zenodo, Dryad, or DataVerse). An example statement could resemble the following: All data and code for this work are available from the Dryad Digital Repository, \citealt{CookEtAl2015}). + +\section*{Appendix A: Additional Methods and Parameters} + +% In most cases, authors should typeset supplementary material in a separate, +% author-supplied PDF. For author-supplied PDFs, please consult the +% AmNat_supp_template.tex document, available from +% https://www.journals.uchicago.edu/journals/an/instruct +% +% If you want to use cross-references within the supplemental TeX file, +% it may be helpful to \usepackage{xr} and include the command +% \externaldocument{name-of-supplemental-tex-file} +% +% The Appendix instructions below apply to cases in which +% a brief appendix is to appear in print after the main body of the article. +% That notably includes descriptions of methods, tables defining parameters, +% and other material necessary for reproducing the MS's results. +% +% Please reset counters for the appendix (thus normally figure A1, +% figure A2, table A1, etc.). +% +% Most AmNat articles have no more than one print appendix. If your article +% has more than one, counters for each appendix should match the letter of +% that appendix. For example, tables in Appendix B should be numbered table B1, % table C2, etc. This applies to tables, equations, and figures. +% +% It's better not to use the \appendix command, because we have some +% formatting peculiarities that \appendix conflicts with. + +\renewcommand{\theequation}{A\arabic{equation}} +% redefine the command that creates the equation number. +\renewcommand{\thetable}{A\arabic{table}} +\setcounter{equation}{0} % reset counter +\setcounter{figure}{0} +\setcounter{table}{0} + +\subsection*{Fox--dog encounters through the ages} + +The quick red fox jumps over the lazy brown dog. The quick red fox has always jumped over the lazy brown dog. The quick red fox began jumping over the lazy brown dog in the 19th century and has never ceased from so jumping, as we shall see in figure~\ref{Fig:Jumps}. But there can be surprises (figure~\ref{Fig:JumpsOk}). + +If the order and location of figures is not otherwise clear, feel free to include explanatory dummy text like this: + +[Figure A1 goes here.] + +[Figure A2 goes here.] + +\subsection*{Further insights} + +Tables in the appendices can appear in the appendix text (see table~\ref{Table:Rivers} for an example), unlike appendix figure legends which should be grouped at the end of the document together with the other figure legends. + +\begin{table}[h] +\caption{Various rivers, cities, and animals} +\label{Table:Rivers} +\centering +\begin{tabular}{lll}\hline +River & City & Animal \\ \hline +Chicago & Chicago & Raccoon \\ +Des Plaines & Joliet & Coyote \\ +Illinois & Peoria & Cardinal \\ +Kankakee & Bourbonnais & White-tailed deer \\ +Mississippi & Galena & Bald eagle \\ \hline +\end{tabular} +\bigskip{} +\\ +{\footnotesize Note: See table~\ref{Table:Founders} below for further table formatting hints.} +\end{table} + +Lorem ipsum dolor sit amet, as we have seen in figures~\ref{Fig:Jumps} and \ref{Fig:JumpsOk}. + + +%%%%%%%%%%%%%%%%%%%%% +% Bibliography +%%%%%%%%%%%%%%%%%%%%% +% You can either type your references following the examples below, or +% compile your BiBTeX database and paste the contents of your .bbl file +% here. The amnatnat.bst style file should work for this---but please +% let us know if you run into any hitches with it! +% +% If you upload a .bib file with your submission, please upload the .bbl +% file as well; this will be required for typesetting. +% +% The list below includes sample journal articles, book chapters, and +% Dryad references. + +\begin{thebibliography}{} + +\bibitem[{Cook et~al.(2015)Cook, Collaborator, and Expert}]{CookEtAl2015} +Cook, O.~E., G.~H. Collaborator, and A.~Q. Expert. 2015. +\newblock Data from: Template and guidelines for using \LaTeX{} in \textit{The American Naturalist}. +\newblock American Naturalist, Dryad Digital Repository, https://dx.doi.org/10.5061/dryad.XYZAB123. + +\bibitem[{Darwin(1859)Darwin}]{OriginSpec} +Darwin, C. 1859. +\newblock On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. +\newblock J.~Murray, London. + +\bibitem[{Davis et~al.(2011)Davis, Brakora, and Lee}]{DavisEtAl2011} +Davis, E.~B., K.~A. Brakora, and A.~H. Lee. 2011. +\newblock Evolution of ruminant headgear: a review. +\newblock Proceedings of the Royal Society~B 278:2857--2865. + +\bibitem[{Inglis et~al.(2011)Inglis, Roberts, Gardner, and Buckling}]{Ing11} +Inglis, R.~F., P.~G. Roberts, A.~Gardner, and A.~Buckling. 2011. +\newblock Spite and the scale of competition in \textit{Pseudomonas + aeruginosa}. +\newblock American Naturalist 178:276--285. + +\bibitem[{Fastovsky(2009)Fastovsky}]{LemKapEx07} +Fastovsky, D.~E. 2009. +\newblock Ideas in dinosaur paleontology: resonating to social and political context. +\newblock Pages 239--253 \emph{in} D. Sepkoski and M. Ruse, eds. The Paleobiological Revolution. University of Chicago Press, Chicago~IL. + +\bibitem[{Xiao et~al.(2015)Xiao, McGlinn, and White}]{Xiao2015} +Xiao, X., D.~J. McGlinn, and E.~P. White. 2015. +\newblock A strong test of the maximum entropy theory of ecology. +\newblock American Naturalist 185:E705--E80. + +\section*{References Cited Only in the Online Enhancements} + +% This section is for works cited in your supplemental PDF but +% not in the main text. + +\bibitem[{Tytler(1759)Tytler}]{tytler-mqos} +Tytler, W. 1759. +\newblock The Inquiry, Historical and Critical, into the Evidence against Mary Queen of Scots, and an Examination of the Histories of Dr. Robertson and David Hume with respect to that Evidence. +\newblock W.~Creech, Edinburgh. + +\end{thebibliography} + +\newpage{} + +\section*{Tables} +\renewcommand{\thetable}{\arabic{table}} +\setcounter{table}{0} + +\begin{table}[h] +\caption{Founders of \textit{The~American Naturalist}} +\label{Table:Founders} +\centering +\begin{tabular}{lll}\hline +Early editor & Years with the journal \\ \hline +Alpheus S. Packard Jr. & 1867--1886 \\ +Frederick W. Putnam & 1867--1874 \\ +Edward S. Morse & 1867--1871 \\ +Alpheus Hyatt & 1867--1871 \\ +Edward Drinker Cope$^a$ & 1878--1897 \\ +J.~S. Kingsley & 1887--1896 \\ \hline +\end{tabular} +\bigskip{} +\\ +{\footnotesize Note: Table titles should be short. Further details should go in a `notes' area after the tabular environment, like this. $^a$ Published the first description of \textit{Dimetrodon}.} +\end{table} + +\newpage{} + +\section*{Figure legends} + +\begin{figure}[h!] +%\includegraphics{horn-of-okapi} +\caption{Figure legends can be longer than the titles of tables. However, they should not be excessively long---in most cases, they should be no more than 100 words each.} +\label{Fig:OkapiHorn} +\end{figure} + + + +\begin{figure}[h!] +%\includegraphics{elegance} +\caption{In this way, figure legends can be listed at the end of the document, with references that work, even though the graphic itself should be included for final files after acceptance. Instead, upload the relevant figure files separately to Editorial Manager; Editorial Manager should insert them at the end of the PDF automatically.} +\label{Fig:AnotherFigure} +\end{figure} + +% Figure legends for any print appendices you might have. + +\renewcommand{\thefigure}{A\arabic{figure}} +\setcounter{figure}{0} + +\begin{figure}[h!] +%\includegraphics{jumps20m} +\caption{\textit{A}, the quick red fox proceeding to jump 20~m straight into the air over not one, but several lazy dogs. \textit{B}, the quick red fox landing gracefully despite the skepticism of naysayers.} +\label{Fig:Jumps} +\end{figure} + +\begin{figure}[h!] +%\includegraphics{jumps20m} +\caption{The quicker the red fox jumps, the likelier it is to land near an okapi. For further details, see \citet{LemKapEx07}.} +\label{Fig:JumpsOk} +\end{figure} + + +%%%%%%%%%%%%%%%%%%%%% +% Videos +%%%%%%%%%%%%%%%%%%%%% +% If you have videos, journal style for them is generally similar to that for +% figures. + +%%%%% Include the text below if you have videos + +\renewcommand{\figurename}{Video} +\renewcommand{\thefigure}{S\arabic{figure}} +\setcounter{figure}{0} + +\begin{figure}[h!] +%\includegraphics{VideoScreengrab.jpg} +\caption{Video legends can follow the same principles as figure legends. Counters should be set and reset so that videos and figures are enumerated separately.} +\label{VideoExample} +\end{figure} + +\renewcommand{\figurename}{Figure} +\setcounter{figure}{1} + +%%%%% Include the above if you have videos + + +\end{document} diff --git a/docs/ipm_comparison_ms.pdf b/docs/ipm_comparison_ms.pdf index b414f3e..4448aa9 100644 Binary files a/docs/ipm_comparison_ms.pdf and b/docs/ipm_comparison_ms.pdf differ diff --git a/docs/ipm_comparison_ms.qmd b/docs/ipm_comparison_ms.qmd index 9623c76..fa51bd1 100644 --- a/docs/ipm_comparison_ms.qmd +++ b/docs/ipm_comparison_ms.qmd @@ -36,11 +36,13 @@ csl: "templates/the-american-naturalist.csl" # Insert path for the bib-style # These are the highlights format: pdf: + # template: AmNat_MS_template.tex + # documentclass: scrarticle + documentclass: article number-sections: false colorlinks: true keeptex: true - fontsize: 11pt - documentclass: article + fontsize: 12pt # the following line is to render the aaffiliations in pdf, which is not default in quarto, see # https://stackoverflow.com/questions/75040607/why-do-affiliations-not-show-up-anywhere-in-the-pdf-output-of-quarto template-partials: @@ -59,6 +61,10 @@ format: \usepackage{titlesec} \usepackage[sc]{mathpazo} %Like Palatino with extensive math support \usepackage[utf8]{inputenc} + \usepackage{parskip} + \setlength{\parskip}{1pt} % 1ex plus 0.5ex minus 0.2ex} + \setlength{\parindent}{0pt} + #\sectionfont{\color{black}\fontsize{12}{16.8}\selectfont} #\subsectionfont{\color{black}\fontsize{12}{16.8}\selectfont} @@ -136,6 +142,18 @@ withr::with_dir(here(), { Text of 150 words max summarizing this amazing paper. +\bigskip + +**Keywords:** demography, environmental stochasticity, integral projection models, lagged effects, structured population models, population dynamics + +\bigskip + +**Manuscript elements:** Figure\~1, figure\~2, table\~1, appendix\~A.. + +\bigskip + +**Manuscript type:** e-note + \pagebreak ## Introduction @@ -146,22 +164,33 @@ Text of 150 words max summarizing this amazing paper. 1. Two types of structured population models - matrix models [@leslie1945use; @caswell2001] and integral projection models [@ellnerIntegralProjectionModels2006] - are fundamental frameworks used to study demography and population dynamics. 2. Their flexibility, in concert with a rapidly growing suite of software, data, and other resources [@ellnerDatadrivenModellingStructured2016; @levinIpmrFlexibleImplementation2021; @salguero-gomezCOMPADREPlantMatrix2015], have facilitated their use to study a wide range of topics in ecology, evolution, and conservation [@ellnerDatadrivenModellingStructured2016; @morrisQuantitativeConservationBiology2002; @croneHowPlantEcologists2011]. -3. While recent mathematical and statistical developments have expanded the scope of these applications [e.g., @brooksStatisticalModelingPatterns2019; @reesEvolvingIntegralProjection2016], a number of technical challenges remain. -4. While many of these relate to general issues surrounding model development and validation [e.g., @williams2012avoiding], others stem from the fundamental challenge of using mathematical models - albeit highly advanced ones - to describe and analyze complex biological systems. +3. Mathematical and statistical advances have rapidly expand the scope of questions that can be addressed with these models [e.g., @brooksStatisticalModelingPatterns2019; @reesEvolvingIntegralProjection2016]. +4. However, there are still several fundamental questions for which these models are not yet readily applied, or for which it is unclear how potential alternative approaches will shape model results [e.g., @williams2012avoiding]. + + + + ### Paragraph 2: Challenge of lagged effects -1. Once such biological challenge is the implementation of alagged effects. It has long been recognized that there is the potential for lagged effects. -2. Including lagged effects in models has been a major technical challenge, but there are now multiple approaches for doing so. -3. The studies assessing the potential for lagged effects on vital rates find that they indeed appear to be prevalent [@eversLaggedDormantSeason2021; @scottDelayedEffectsClimate2022]. +1. One example of such a process is *Delayed Life-history Events* (i.e., DLHEs), also known as *Lagged Effects*. +2. Lagged effects are those in which the demographic vital rates observed in a given year are influenced -- or even determined by -- past environmental conditions. +3. For instance, environmental conditions during juvenile development can shape the expression of traits (e.g., defensive spikes on *Daphnia*) that determine adult survival. +4. Alternatively, the physiological mechanisms responsible for a vital rate can take an extended period of time to complete (e.g., bud formation in \_\_\_\_\_ can begin 1-2 years before flowers appear). +5. Vital rates can even be influenced by environmental conditions during the parental life-cycle or historical trade-offs between vital rates (e.g., delayed costs of reproduction, competition-colonization trade-offs). +6. Although these lagged effects could potentially have major consequences for population dynamics [@beckermanPopulationDynamicConsequences2002], their impacts remain poorly understood for two primary reasons. +7. The first is the empirical challenge of designing studies to quantify lagged responses and evaluate their potential drivers [@kussEvolutionaryDemographyLonglived2008a]. +8. The second is the technical challenge of incorporating these complex or poorly understood biological processes in demographic models; doing often renders them less parameterizable, tractable, or broadly applicable. ### Paragraph 3: Why does it matter when modeling? -1. Lagged effects could be different in different habitat types. -2. This could be a big reason for differences between habitats. -3. Could also be important for stochastic vs. deterministic models. -4. Here we... -5. We conducted these analyses with both deterministic and stochastic IPMs. +1. Recent years have seen a surge in new approaches for doing so, including ***,*** \_, and \_\_\_\_. +2. Studies assessing potential for lagged effects on vital rates find that they indeed appear to be prevalent [@eversLaggedDormantSeason2021; @scottDelayedEffectsClimate2022]. +3. Lagged effects could be different in different habitat types. +4. This could be a big reason for differences between habitats. +5. Could also be important for stochastic vs. deterministic models. +6. Here we... +7. We conducted these analyses with both deterministic and stochastic IPMs. ## Methods @@ -477,5 +506,3 @@ knitr::include_graphics(path, rel_path = FALSE) knitr::include_graphics(here(fig_pop_states), rel_path = FALSE) ``` - -\`\`\`\` diff --git a/docs/lagged-ipms-ms.bib b/docs/lagged-ipms-ms.bib index 5ed4d49..7143962 100644 --- a/docs/lagged-ipms-ms.bib +++ b/docs/lagged-ipms-ms.bib @@ -21,7 +21,7 @@ @article{croneHowPlantEcologists2011 journal = {Ecology Letters}, author = {Crone, E. E. and Menges, E. S. and Ellis, M. M. and Bell, T. and Bierzychudek, P. and Ehrlen, J. and Kaye, T. N. and Knight, T. M. and Lesica, P. and Morris, W. F. and Oostermeijer, G. and Quintana-Ascencio, P. F. and Stanley, A. and Ticktin, T. and Valverde, T. and Williams, J. L.}, year = {2011}, - keywords = {analysis, assessment, biology, conservation, demography, dynamics, ecological, evolution, extinction, forecasting, growth, harvest, life-history, matrix, meaningful, models, plant, population, probability, projection, rate, risk, sensitivity, viability}, + keywords = {biology, conservation, matrix, plant, demography, sensitivity, evolution, life-history, growth, dynamics, extinction, models, population, rate, projection, viability, analysis, harvest, assessment, ecological, forecasting, meaningful, probability, risk}, pages = {1--8}, } @@ -69,7 +69,7 @@ @article{reesIntegralProjectionModels2009 journal = {Ecological Monographs}, author = {Rees, M. and Ellner, S. P.}, year = {2009}, - keywords = {adaptive, analysis, carlina, carlina-vulgaris, dynamics, environment, evolution, evolutionarily, experiment, fitness, flowering, fluctuating, forecasting, function-valued, growth, integral, life, mixed, model, models, population, projection, random, rate, response, selection, sensitivity, size, stable, stochastic, strategies, structured, table, temporal, topography, traits, variability, variable, vulgaris}, + keywords = {model, variability, sensitivity, evolution, size, growth, dynamics, selection, models, population, mixed, rate, traits, random, life, stochastic, temporal, integral, projection, analysis, environment, structured, fitness, forecasting, response, table, variable, stable, flowering, fluctuating, function-valued, experiment, strategies, adaptive, evolutionarily, carlina-vulgaris, carlina, topography, vulgaris}, pages = {575--594}, } @@ -83,11 +83,25 @@ @article{reesEvolvingIntegralProjection2016 journal = {Methods in Ecology and Evolution}, author = {Rees, M. and Ellner, S. P.}, year = {2016}, - keywords = {biology, decisions, ecology, environment, evolutionary, flowering, fluctuating, function-valued, genetic-variation, genetics, life-history, microevolution, modelling, oenothera-glazioviana, population, population-dynamics, populations, quantitative, structured, traits, variable}, + keywords = {biology, population-dynamics, populations, life-history, population, traits, ecology, environment, evolutionary, structured, decisions, variable, flowering, fluctuating, function-valued, genetic-variation, genetics, microevolution, modelling, oenothera-glazioviana, quantitative}, pages = {157--170}, file = {Rees and Ellner - 2016 - Evolving integral projection models evolutionary .pdf:/Users/emiliobruna/Zotero/storage/YQ9JD9QC/Rees and Ellner - 2016 - Evolving integral projection models evolutionary .pdf:application/pdf}, } +@article{crileyYearProductionHigh1994, + series = {New ornamental crops and the market for floricultural products}, + title = {Year around production with high yields may be a possibility for \textit{{Heliconia} chartacea}}, + volume = {397}, + url = {https://doi.org/10.17660/ActaHortic.1995.397.7}, + doi = {10.17660/ActaHortic.1995.397.7}, + journal = {Acta Horticulturae}, + author = {Criley, RA and Lekawatana, S}, + year = {1994}, + note = {tex.ids= criley1994}, + pages = {95--102}, + file = {Criley and Lekawatana - 1994 - Year around production with high yields may be a p.pdf:/Users/emiliobruna/Zotero/storage/D94T8EAZ/Criley and Lekawatana - 1994 - Year around production with high yields may be a p.pdf:application/pdf}, +} + @article{salguero-gomezCOMPADREPlantMatrix2015, title = {The {COMPADRE} {Plant} {Matrix} {Database}: an open online repository for plant demography}, volume = {103}, @@ -103,7 +117,7 @@ @article{salguero-gomezCOMPADREPlantMatrix2015 editor = {Rees, Mark}, month = jan, year = {2015}, - keywords = {access, analyses, and, approach, big, climate-change, community, comparative, data, desert, dynamics, elasticity, evolution, growth, herb, integral, life-history, matrix, model, models, open, perennial, plant, plants, population, population-growth-rate, populations, projection, rate, sensitivity, sensitivity-analysis, stage-structured, transient, viability}, + keywords = {community, populations, climate-change, matrix, model, plant, elasticity, sensitivity, evolution, life-history, growth, plants, dynamics, population-growth-rate, sensitivity-analysis, models, desert, herb, population, and, comparative, rate, perennial, access, analyses, approach, big, data, integral, open, projection, stage-structured, transient, viability}, pages = {202--218}, file = {Salguero‐Gómez et al. - 2015 - The COMPADRE Plant Matrix Database an open online.pdf:/Users/emiliobruna/Zotero/storage/6CQPZP38/Salguero‐Gómez et al. - 2015 - The COMPADRE Plant Matrix Database an open online.pdf:application/pdf}, } @@ -261,7 +275,7 @@ @article{xavierDailyGriddedMeteorological2016 author = {Xavier, Alexandre C. and King, Carey W. and Scanlon, Bridget R.}, year = {2016}, note = {tex.copyright: © 2015 Royal Meteorological Society}, - keywords = {Brazil, data set, evapotranspiration, gridded data, interpolation, meteorological variables, precipitation, read}, + keywords = {Brazil, read, gridded data, precipitation, data set, evapotranspiration, interpolation, meteorological variables}, pages = {2644--2659}, } @@ -284,7 +298,7 @@ @article{levinIpmrFlexibleImplementation2021 journal = {Methods in Ecology and Evolution}, author = {Levin, Sam C. and Childs, Dylan Z. and Compagnoni, Aldo and Evers, Sanne and Knight, Tiffany M. and Salguero-Gómez, Roberto}, year = {2021}, - keywords = {elasticity, integral projection model, life history, population dynamics, population growth rate, sensitivity, structured populations}, + keywords = {integral projection model, population dynamics, elasticity, life history, population growth rate, sensitivity, structured populations}, pages = {1826--1834}, } @@ -311,7 +325,7 @@ @article{metcalfStatisticalModellingAnnual2015 author = {Metcalf, C. Jessica E. and Ellner, Stephen P. and Childs, Dylan Z. and Salguero-Gómez, Roberto and Merow, Cory and McMahon, Sean M. and Jongejans, Eelke and Rees, Mark}, year = {2015}, note = {tex.copyright: © 2015 The Authors. Methods in Ecology and Evolution © 2015 British Ecological Society}, - keywords = {covariation, integral projection model, population growth rate, population projection, population viability, random vs. fixed effects, read, sampling effects, stochastic simulations}, + keywords = {integral projection model, population growth rate, read, covariation, population viability, population projection, random vs. fixed effects, sampling effects, stochastic simulations}, pages = {1007--1017}, } @@ -340,7 +354,7 @@ @article{brunaEffectMutualistPartner2014a note = {Place: 111 RIVER ST, HOBOKEN 07030-5774, NJ USA Publisher: WILEY Type: Article}, - keywords = {Azteca, Crematogaster, integral projection model, lambda, life-table response experiment, Maieta, Melastomataceae}, + keywords = {integral projection model, lambda, life-table response experiment, Crematogaster, Maieta, Melastomataceae, Azteca}, pages = {3237--3243}, file = {Full Text PDF:/Users/emiliobruna/Zotero/storage/M6B48ATL/Bruna et al. - 2014 - Effect of mutualist partner identity on plant demo.pdf:application/pdf;Snapshot:/Users/emiliobruna/Zotero/storage/9QFAI6IQ/14-0481.html:text/html}, } @@ -366,3 +380,423 @@ @article{williams2012avoiding note = {Publisher: Wiley Online Library}, pages = {2008--2014}, } + +@article{combrinkCurrentTimelaggedEffects2021, + title = {Current and time-lagged effects of climate on innate immunity in two sympatric snake species}, + volume = {11}, + copyright = {© 2021 The Authors. Ecology and Evolution published by John Wiley \& Sons Ltd.}, + issn = {2045-7758}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.7273}, + doi = {10.1002/ece3.7273}, + abstract = {Changing environments result in alterations at all levels of biological organization, from genetics to physiology to demography. The increasing frequency of droughts worldwide is associated with higher temperatures and reduced precipitation that can impact population persistence via effects on individual immune function and survival. We examined the effects of annual climate variation on immunity in two sympatric species of garter snakes from four populations in California over a seven-year period that included the record-breaking drought. We examined three indices of innate immunity: bactericidal competence (BC), natural antibodies (NABs), and complement-mediated lysis (CL). Precipitation was the only climatic variable explaining variation in immune function: spring precipitation of the current year was positively correlated to Thamnophis sirtalis BC and NABs, whereas spring precipitation of the previous year was positively correlated to T. elegans BC and NABs. This suggests that T. elegans experiences a physiological time-lag in response to reduced precipitation, which may reflect lack of capital for investment in immunity in the year following a dry year. In general, our findings demonstrate compelling evidence that climate can influence wild populations through effects on physiological processes, suggesting that physiological indices such as these may offer valuable opportunities for monitoring the effects of climate.}, + language = {en}, + number = {7}, + urldate = {2024-09-04}, + journal = {Ecology and Evolution}, + author = {Combrink, Lucia L. and Bronikowski, Anne M. and Miller, David A. W. and Sparkman, Amanda M.}, + year = {2021}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.7273}, + keywords = {drought, precipitation, temperature, garter snakes, innate immunity, sympatry}, + pages = {3239--3250}, + file = {Full Text PDF:/Users/emiliobruna/Zotero/storage/Y2AYB5VQ/Combrink et al. - 2021 - Current and time-lagged effects of climate on inna.pdf:application/pdf;Snapshot:/Users/emiliobruna/Zotero/storage/2NV7F7IN/ece3.html:text/html}, +} + +@article{oconnorLinkingPhysiologicalEffects2006, + title = {Linking physiological effects on activity and resource use to population level phenomena}, + volume = {46}, + issn = {1540-7063}, + url = {https://doi.org/10.1093/icb/icl031}, + doi = {10.1093/icb/icl031}, + abstract = {We present an approach to delineating physiological effects on population level processes by modeling the activity and resource budgets of animals. Physiology and its environmental forcing functions are assumed to affect both the total time available for activity and foraging and the resource budgets by affecting resource acquisition, costs, and handling. We extend the earlier model of Dunham and others (1989) and translate it into a computational algorithm. To satisfy conservation needs for accuracy, wide applicability, and rapid deployment, the model is relatively simple, uses as much data on the focal organism as possible, is mechanistically driven, and can be adapted to new organisms by using data for the new species, or the best available approximations to those data. We present 2 applications of the modeling approach. First, we consider a system with substantial information available, canyon lizards (Sceloporus merriami) studied by Dunham and colleagues in west Texas. In this case the focus is on integration of numerous inputs and the ability of the model to produce predictions that approximate counterintuitive empirical patterns. By using the wealth of specific data available, the model outperforms previous attempts at explanation of those patterns. Next, we consider a system with much less available information (forest-dwelling semi-fossorial frogs). The question here is how hydric conditions can become limiting. A model of evaporation from frogs buried in leaf litter was incorporated and it demonstrates how rainfall patterns can both supply water and put the frogs at risk of critical dehydration.}, + number = {6}, + urldate = {2024-09-04}, + journal = {Integrative and Comparative Biology}, + author = {O'Connor, Michael P. and Sieg, Annette E. and Dunham, Arthur E.}, + month = dec, + year = {2006}, + pages = {1093--1109}, + file = {Full Text PDF:/Users/emiliobruna/Zotero/storage/X5VXZADJ/O'Connor et al. - 2006 - Linking physiological effects on activity and reso.pdf:application/pdf}, +} + +@article{biglerDailyMaximumTemperatures2019, + title = {Daily {Maximum} {Temperatures} {Induce} {Lagged} {Effects} on {Leaf} {Unfolding} in {Temperate} {Woody} {Species} {Across} {Large} {Elevational} {Gradients}}, + volume = {10}, + issn = {1664-462X}, + url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2019.00398/full}, + doi = {10.3389/fpls.2019.00398}, + abstract = {{\textless}p{\textgreater}The timing of leaf unfolding in temperate woody species is predominantly controlled by the seasonal course of temperature in late winter and early spring. However, quantifying lagged temperature effects on spring phenology is still challenging. Here, we aimed at investigating lagged and potentially non-linear effects of daily maximum temperatures on the probability of leaf unfolding in temperate woody species growing across large elevational gradients. We analyzed 5280 observations of leaf-out time of four tree species (European beech, horse chestnut, European larch, Norway spruce) and one shrub species (common hazel) that were recorded by volunteers over 40 years at 42 locations in Switzerland. We used a case-crossover sampling design to match leaf-out dates with control dates (i.e., dates before or after leaf-out), and analyzed these data with conditional logistic regression accounting for lagged temperature effects over 60 days. Multivariate meta-analyses were used to synthesize lagged temperature and elevational effects on leaf unfolding across multiple phenological stations. Temperature effects on the probability of leaf unfolding were largest at relatively short lags (i.e., within ca. 10 days) and decreased with increasing lags. Short- to mid-term effects (i.e., within ca. 10 to 20 days) were larger for late-leafing species known to be photoperiod-sensitive (beech, Norway spruce). Temperature effects increased for the broadleaved species (horse chestnut, hazel, beech) with decreasing elevation, particularly within ca. 10 to 40 days, i.e., leaf unfolding occurs more rapidly at low elevations for a given daily maximum temperature. Our novel findings provide evidence of cumulative and long-term temperature effects on leaf unfolding, whereby the efficiency of relatively high temperatures to trigger leaf-out becomes higher shortly before bud burst. These lagged associations between temperature and leaf unfolding improve our understanding of phenological responses across temperate woody species with differing ecological requirements that occur along elevational gradients.{\textless}/p{\textgreater}}, + language = {English}, + urldate = {2024-09-04}, + journal = {Frontiers in Plant Science}, + author = {Bigler, Christof and Vitasse, Yann}, + month = mar, + year = {2019}, + note = {Publisher: Frontiers}, + keywords = {Phenology, elevation, Broadleaved species, Conifers, Distributed lag models, Lag effects, Maximum temperature, Multivariate meta-analysis}, + file = {Full Text:/Users/emiliobruna/Zotero/storage/AVVGZJBT/Bigler and Vitasse - 2019 - Daily Maximum Temperatures Induce Lagged Effects o.pdf:application/pdf}, +} + +@article{rastetterTimeLagsInsights2021, + title = {Time lags: insights from the {U}.{S}. {Long} {Term} {Ecological} {Research} {Network}}, + volume = {12}, + copyright = {© 2021 The Authors.}, + issn = {2150-8925}, + shorttitle = {Time lags}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ecs2.3431}, + doi = {10.1002/ecs2.3431}, + abstract = {Ecosystems across the United States are changing in complex ways that are difficult to predict. Coordinated long-term research and analysis are required to assess how these changes will affect a diverse array of ecosystem services. This paper is part of a series that is a product of a synthesis effort of the U.S. National Science Foundation’s Long Term Ecological Research (LTER) network. This effort revealed that each LTER site had at least one compelling scientific case study about “what their site would look like” in 50 or 100 yr. As the site results were prepared, themes emerged, and the case studies were grouped into separate papers along five themes: state change, connectivity, resilience, time lags, and cascading effects and compiled into this special issue. This paper addresses the time lags theme with five examples from diverse biomes including tundra (Arctic), coastal upwelling (California Current Ecosystem), montane forests (Coweeta), and Everglades freshwater and coastal wetlands (Florida Coastal Everglades) LTER sites. Its objective is to demonstrate the importance of different types of time lags, in different kinds of ecosystems, as drivers of ecosystem structure and function and how these can effectively be addressed with long-term studies. The concept that slow, interactive, compounded changes can have dramatic effects on ecosystem structure, function, services, and future scenarios is apparent in many systems, but they are difficult to quantify and predict. The case studies presented here illustrate the expanding scope of thinking about time lags within the LTER network and beyond. Specifically, they examine what variables are best indicators of lagged changes in arctic tundra, how progressive ocean warming can have profound effects on zooplankton and phytoplankton in waters off the California coast, how a series of species changes over many decades can affect Eastern deciduous forests, and how infrequent, extreme cold spells and storms can have enduring effects on fish populations and wetland vegetation along the Southeast coast and the Gulf of Mexico. The case studies highlight the need for a diverse set of LTER (and other research networks) sites to sort out the multiple components of time lag effects in ecosystems.}, + language = {en}, + number = {5}, + urldate = {2024-09-04}, + journal = {Ecosphere}, + author = {Rastetter, Edward B. and Ohman, Mark D. and Elliott, Katherine J. and Rehage, J. S. and Rivera-Monroy, Victor H. and Boucek, R. E. and Castañeda-Moya, Edward and Danielson, Tess M. and Gough, Laura and Groffman, Peter M. and Jackson, C. Rhett and Miniat, Chelcy Ford and Shaver, Gaius R.}, + year = {2021}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ecs2.3431}, + keywords = {climate change, climate change detection, climate signal filtering, ecosystem response, Special Feature: Forecasting Earth’s Ecosystems with Long-Term Ecological Research}, + pages = {e03431}, + file = {Full Text PDF:/Users/emiliobruna/Zotero/storage/3KUQTFHD/Rastetter et al. - 2021 - Time lags insights from the U.S. Long Term Ecolog.pdf:application/pdf;Snapshot:/Users/emiliobruna/Zotero/storage/3M6HIZMN/ecs2.html:text/html}, +} + +@article{dudneyLaggingHaveWe2017, + title = {Lagging behind: have we overlooked previous-year rainfall effects in annual grasslands?}, + volume = {105}, + copyright = {© 2016 The Authors. Journal of Ecology © 2016 British Ecological Society}, + issn = {1365-2745}, + shorttitle = {Lagging behind}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1365-2745.12671}, + doi = {10.1111/1365-2745.12671}, + abstract = {Rainfall is a key determinant of production and composition in arid and semi-arid systems. Long-term studies relating composition and water availability primarily focus on current-year precipitation patterns, though mounting evidence highlights the importance of previous-year rainfall particularly in grasslands dominated by perennial species. The extent to which lagged precipitation effects occur in annual grasslands, however, remains largely unexplored. We pair a long-term study with two manipulative experiments to identify patterns and mechanisms of lagged precipitation effects in annual grasslands. The long-term study captured variation in functional group (exotic annual forbs and grasses) abundance and precipitation across 8 years at three northern California grassland sites. We then tested whether lagged rainfall effects were created through seed production and litter (residual dry matter, RDM) by manipulating rainfall and litter, respectively. Rainfall from the previous-year growing season (both seasonal and total rainfall) shifted functional group abundance. High lagged rainfall was associated with increased grass and decreased forb abundance the following year. Current-year seasonal rainfall also influenced species composition, with winter rain increasing forb and decreasing grass abundance. Lagged precipitation effects were generally stronger for forbs than for grasses. Our experimental studies provided evidence for two mechanisms that contributed to lagged effects in annual grasslands. Higher rainfall increased seed production for grasses, which translated to more germinable seed the following year. Higher rainfall also increased biomass production and RDM, which benefited grasses and reduced forb abundance. Synthesis. Our results highlight the importance of previous-year precipitation in structuring annual community composition and suggest two important biotic pathways, seed rain and RDM, that regulate lagged community responses to rainfall. Incorporating lagged effects into models of grassland diversity and productivity could improve predictions of climate change impacts in annual grasslands.}, + language = {en}, + number = {2}, + urldate = {2024-09-04}, + journal = {Journal of Ecology}, + author = {Dudney, Joan and Hallett, Lauren M. and Larios, Loralee and Farrer, Emily C. and Spotswood, Erica N. and Stein, Claudia and Suding, Katharine N.}, + year = {2017}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2745.12671}, + keywords = {legacy effects, plant population and community dynamics, lagged effects, litter dynamics, plant–climate interactions, functional groups, annual plant seed production, determinants of plant community diversity and structure, precipitation effects, species responses to weather}, + pages = {484--495}, + file = {Full Text PDF:/Users/emiliobruna/Zotero/storage/3DA8RSPE/Dudney et al. - 2017 - Lagging behind have we overlooked previous-year r.pdf:application/pdf;Snapshot:/Users/emiliobruna/Zotero/storage/97KRFIV2/1365-2745.html:text/html}, +} + +@article{pearseLaggedEffectsEarlyseason2015, + title = {Lagged effects of early-season herbivores on valley oak fecundity}, + volume = {178}, + issn = {1432-1939}, + url = {https://doi.org/10.1007/s00442-014-3193-2}, + doi = {10.1007/s00442-014-3193-2}, + abstract = {The seasonal match between folivore and leaf phenology affects the annual success of arboreal folivore populations because many folivores exploit developing leaves, which are an ephemeral resource. One strategy for folivores to exploit early-season leaves is to anticipate their emergence. The consequence of this behavior for trees is that individuals that set leaves earlier may experience greater rates of folivore damage, with potential negative fitness consequences. To test this hypothesis, we surveyed the early-season phenology, insect folivore damage, and acorn crop of a population of valley oaks (Quercus lobata) over a 3-year period. We found that trees that set leaves earlier experienced greater rates of folivore damage than trees that set leaves later in the season. In addition, we observed a lagged effect of folivore damage on acorn production, whereby trees with greater leaf damage produced fewer acorns in the subsequent year. These results indicate potential negative fitness consequences of earlier leaf phenology. Our study suggests that folivore pressure may be one factor that affects the optimal timing of leaf set in oaks.}, + language = {en}, + number = {2}, + urldate = {2024-09-04}, + journal = {Oecologia}, + author = {Pearse, Ian S. and Funk, Kyle A. and Kraft, Thomas S. and Koenig, Walter D.}, + month = jun, + year = {2015}, + keywords = {Phenology, Herbivory, Quercus, Chionodes, Leaf set}, + pages = {361--368}, + file = {Full Text PDF:/Users/emiliobruna/Zotero/storage/37FGJT3Z/Pearse et al. - 2015 - Lagged effects of early-season herbivores on valle.pdf:application/pdf}, +} + +@article{pirottaIndividualResponsesPopulation2022, + title = {From individual responses to population effects: {Integrating} a decade of multidisciplinary research on blue whales and sonar}, + volume = {25}, + copyright = {© 2022 The Authors. Animal Conservation published by John Wiley \& Sons Ltd on behalf of Zoological Society of London.}, + issn = {1469-1795}, + shorttitle = {From individual responses to population effects}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/acv.12785}, + doi = {10.1111/acv.12785}, + abstract = {As ecosystems transform under climate change and expanding human activities, multidisciplinary integration of empirical research, conceptual frameworks and modelling methods is required to predict, monitor and manage the cascading effects on wildlife populations. For example, exposure to anthropogenic noise can lead to changes in the behaviour and physiology of individual marine mammals, but management is complicated by uncertainties on the long-term effects at a population level. We build on a decade of diverse efforts to demonstrate the strengths of integrating research on multiple stressors for assessing population-level effects. Using the case study of blue whales exposed to military sonar in the eastern north Pacific, we model how behavioural responses and environmental effects induced by climate change affect female survival and reproductive success. Environmental changes were predicted to severely affect vital rates, while the current regime of sonar activities was not. Simulated disturbance had a stronger effect on reproductive success than adult survival, as predicted by life-history theory. We show that information on prey resources is critical for robust predictions, as are data on baseline behavioural patterns, energy budgets, body condition and contextual responses to noise. These results will support effective management of the interactions between sonar operations and blue whales in the study area, while providing pragmatic guidance for future data collection to reduce key uncertainties. Our study provides important lessons for the successful integration of multidisciplinary research to inform the assessment of the effects of noise and other anthropogenic stressors on marine predator populations in the context of a changing environment.}, + language = {en}, + number = {6}, + urldate = {2024-09-04}, + journal = {Animal Conservation}, + author = {Pirotta, E. and Booth, C. G. and Calambokidis, J. and Costa, D. P. and Fahlbusch, J. A. and Friedlaender, A. S. and Goldbogen, J. A. and Harwood, J. and Hazen, E. L. and New, L. and Santora, J. A. and Watwood, S. L. and Wertman, C. and Southall, B. L.}, + year = {2022}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/acv.12785}, + keywords = {climate change, data integration, anthropogenic disturbance, marine mammals, mechanistic modelling, military sonar, population consequences of disturbance, spatial planning}, + pages = {796--810}, + file = {Full Text PDF:/Users/emiliobruna/Zotero/storage/3NDLDC5C/Pirotta et al. - 2022 - From individual responses to population effects I.pdf:application/pdf}, +} + +@article{selasClimaticSeasonalControl2015, + title = {Climatic and seasonal control of annual growth rhythm and flower formation in {Vaccinium} myrtillus ({Ericaceae}), and the impact on annual variation in berry production}, + volume = {148}, + doi = {10.5091/plecevo.2015.1110}, + abstract = {Background and aims – Large variation in annual berry production occurs in Vaccinium myrtillus L., and the variation has been associated with population cycling of many herbivores. Because of its ecological significance, variation in berry production has frequently been related to climatic variables. Methods – In an attempt to elucidate the possible causality of such relations, we have examined the seasonal and climatic control of growth rhythm and flowering performance of V. myrtillus in the field and in a controlled environment. We then reanalysed two long-running time series of berry production, with selected climatic factors as explanatory variables. Key results – Variables retained in the regression models were maximum temperature in June and mean temperature in August–September the year before fruiting, and maximum snow depth in April, minimum temperature in May, and hydrothermal ratio in June–July the current year. These factors could all be directly linked to critical plant processes and events such as timing of floral initiation, winter hardening, avoidance of frost injury during bloom, and drought avoidance in summer. Demonstration of superficial winter dormancy explained the vulnerability of V. myrtillus to winter frost injury and the need for stable snow cover. A highly significant lunisolar index corresponds to oscillations in ionizing cosmic radiation that by some unknown mechanism(s) may affect plant growth and development. Conclusions – We conclude that the explanatory variables obtained in the regression models for annual berry production are causally related to specific physiological mechanisms controlling crucial events in the annual life cycle of V. myrtillus. © 2015 Botanic Garden Meise and Royal Botanical Society of Belgium.}, + journal = {Plant Ecology and Evolution}, + author = {Selås, Vidar and Sønsteby, Anita and Heide, Ola and Opstad, Nina}, + month = nov, + year = {2015}, + pages = {350--360}, + file = {Full Text:/Users/emiliobruna/Zotero/storage/WNZC445Z/Selås et al. - 2015 - Climatic and seasonal control of annual growth rhy.pdf:application/pdf}, +} + +@article{cookEffectsSummerAutumnNutrition2004, + title = {Effects of {Summer}-{Autumn} {Nutrition} and {Parturition} {Date} on {Reproduction} and {Survival} of {Elk}}, + volume = {155}, + copyright = {2004 The Wildlife Society}, + issn = {1938-5455}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.2193/0084-0173%282004%29155%5B1%3AEOSNAP%5D2.0.CO%3B2}, + doi = {10.2193/0084-0173(2004)155[1:EOSNAP]2.0.CO;2}, + abstract = {Abstract: Recent declines in numbers and juvenile recruitment in many elk (Cervus elaphus) herds in the western U.S. has sparked interest in factors that may cause these declines. Inadequate nutrition or delayed parturition, the latter of which may be caused by inadequate numbers of mature bulls (i.e., highly skewed sex ratios), may have separate or synergistic effects on population dynamics and productivity. We evaluated the implications of late parturition and summer-autumn nutrition on reproduction and survival of Rocky Mountain elk (C. e. nelsoni) using a captive herd of 57 cow elk. We induced early (Sep) and late breeding (Oct) and 3 levels of summer-autumn nutrition on the cows. Food was offered ad libitum at 3 levels of digestible energy (DE): high = 2.9-3.0 kcal of DE/g of diets, medium = 2.6-3.0 kcal/g, and low = 2.3-3.0 kcal/g. Within these ranges, DE content was gradually reduced from late June through early November to mimic seasonal changes in the wild. During summer and autumn, we measured calf growth; body mass, nutritional condition, and breeding dynamics of cows; and growth and pregnancy of yearlings. We also measured carry-over (i.e., time-lag) responses including over-winter calf and cow survival and parturition date and birth mass, as functions of previous summer-autumn nutrition and previous parturition date. Between autumn 1995 and spring 1998, we conducted 2 years of parturition-date, summer-autumn nutrition experiments, 2 winters of calf survival experiments, and 1 winter of cow survival experiments. Early birth provided calves with more time to grow before onset of winter. This “head-start” advantage was maintained through late autumn, but its magnitude was diluted in some instances due to faster growth of some late-born calves. Body mass, body fat, and timing and probability of conception by cows in autumn were little influenced by parturition date the previous spring. Summer-autumn nutrition significantly affected calves and their mothers. Growth of calves in the low and medium nutrition groups ceased by mid-September and late October. By December, calves in the high nutrition group were 40\% and 70\% heavier than calves in the medium and low groups, respectively. Cows in the high nutrition group accumulated about 75\% and 300\% more fat than cows in the medium and low groups by mid-October. Eighty percent of cows in the low nutrition group failed to conceive, and those in the medium group bred 10–14 days later than cows in the high group. Summer-autumn nutrition of calves influenced their probability of becoming pregnant as yearlings. Probability of pregnancy approached 100\% for those yearlings that had high summerautumn nutrition as calves and yearlings, despite near starvation their first winter of life. Winter survival of calves was related to their size at the onset of winter. Smaller calves lost more body mass daily than did large calves, and thus they survived fewer days through winter. Summer-autumn nutrition largely determined calf body size at the start of winter and, consequently, determined the proportion of winter survived. Survival of cows over winter was as related to body fat at the onset of winter as it was to nutrition during winter. Carry-over effects of summer-autumn nutrition and parturition date on birth characteristics the following spring were minor. We detected no significant carry-over effect of summer-autumn nutrition or autumn condition on birth mass, although reduced condition in autumn delayed subsequent parturition date. Extent of body fat depletion in cows during the winter-survival experiments in 1998 accounted for 45\% of the variation in parturition date. Ninety percent depletion delayed parturition an average of 34 days. Delayed parturition, of a magnitude expected due to highly skewed sex ratios (3 weeks under extreme conditions), probably has only a weak influence on vital rates of free-ranging elk. In contrast, fat accretion and probability of pregnancy of cows, and growth and overwinter survival of calves, were sensitive to small (10–20\%) differences in DE content of food. Digestible energy levels of our 2 lower nutrition levels reflect DE ranges reported for large ungulate herds during summer and autumn in western North America. Thus, our data suggest that limiting effects of summer-autumn nutrition on populations may be greater than often assumed, perhaps greater than those during winter in some ecosystems, and consequently indicate a need for greater understanding of nutrition's influence on population dynamics and how this influence varies across space and time. To enhance future research, we present animal- and vegetation-based guidelines for evaluating nutritional influences on elk populations.}, + language = {en}, + number = {1}, + urldate = {2024-09-04}, + journal = {Wildlife Monographs}, + author = {Cook, John G. and Johnson, Bruce K. and Cook, Rachel C. and Riggs, Robert A. and Delcurto, Tim and Bryant, Larry D. and Irwin, Larry L.}, + year = {2004}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.2193/0084-0173\%282004\%29155\%5B1\%3AEOSNAP\%5D2.0.CO\%3B2}, + keywords = {population dynamics, growth, habitat, survival, reproduction, Oregon, Cervus elaphus, digestible energy, dry-matter intake, elk, gestation, lactation, nutrition, nutritional condition, pregnancy}, + pages = {1--61}, + file = {Full Text PDF:/Users/emiliobruna/Zotero/storage/F42IHEI9/Cook et al. - 2004 - Effects of Summer-Autumn Nutrition and Parturition.pdf:application/pdf}, +} + +@article{beckermanPopulationDynamicConsequences2002, + title = {Population dynamic consequences of delayed life-history effects}, + volume = {17}, + issn = {0169-5347}, + url = {https://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(02)02469-2}, + doi = {10.1016/S0169-5347(02)02469-2}, + language = {English}, + number = {6}, + urldate = {2024-09-04}, + journal = {Trends in Ecology \& Evolution}, + author = {Beckerman, Andrew and Benton, Tim G. and Ranta, Esa and Kaitala, Veijo and Lundberg, Per}, + month = jun, + year = {2002}, + note = {Publisher: Elsevier}, + keywords = {Ecology, Evolution, Dependence, Population Dynamics, environmental conditions, Cohort Effects, Delayed Density, Delayed Life History Effects, Life History, Maternal Effects}, + pages = {263--269}, + file = {Full Text PDF:/Users/emiliobruna/Zotero/storage/WSINV5SK/Beckerman et al. - 2002 - Population dynamic consequences of delayed life-hi.pdf:application/pdf}, +} + +@article{stuligrossInsecticideExposureReduces2021, + title = {Past insecticide exposure reduces bee reproduction and population growth rate}, + volume = {118}, + url = {https://www.pnas.org/doi/abs/10.1073/pnas.2109909118}, + doi = {10.1073/pnas.2109909118}, + abstract = {Pesticides are linked to global insect declines, with impacts on biodiversity and essential ecosystem services. In addition to well-documented direct impacts of pesticides at the current stage or time, potential delayed “carryover” effects from past exposure at a different life stage may augment impacts on individuals and populations. We investigated the effects of current exposure and the carryover effects of past insecticide exposure on the individual vital rates and population growth of the solitary bee, Osmia lignaria. Bees in flight cages freely foraged on wildflowers, some treated with the common insecticide, imidacloprid, in a fully crossed design over 2 y, with insecticide exposure or no exposure in each year. Insecticide exposure directly to foraging adults and via carryover effects from past exposure reduced reproduction. Repeated exposure across 2 y additively impaired individual performance, leading to a nearly fourfold reduction in bee population growth. Exposure to even a single insecticide application can have persistent effects on vital rates and can reduce population growth for multiple generations. Carryover effects had profound implications for population persistence and must be considered in risk assessment, conservation, and management decisions for pollinators to mitigate the effects of insecticide exposure.}, + number = {48}, + urldate = {2024-09-04}, + journal = {Proceedings of the National Academy of Sciences}, + author = {Stuligross, Clara and Williams, Neal M.}, + month = nov, + year = {2021}, + note = {Publisher: Proceedings of the National Academy of Sciences}, + pages = {e2109909118}, + file = {Full Text PDF:/Users/emiliobruna/Zotero/storage/UBTF4JIH/Stuligross and Williams - 2021 - Past insecticide exposure reduces bee reproduction.pdf:application/pdf}, +} + +@article{douhardFitnessConsequencesEnvironmental2014, + title = {Fitness consequences of environmental conditions at different life stages in a long-lived vertebrate}, + volume = {281}, + url = {https://royalsocietypublishing.org/doi/full/10.1098/rspb.2014.0276}, + doi = {10.1098/rspb.2014.0276}, + abstract = {The predictive adaptive response (PAR) hypothesis proposes that animals adjust their physiology and developmental trajectory during early life in anticipation of their future environments. Accordingly, when environmental conditions in early life match environmental conditions during adulthood, individual fitness should be greater. Here, we test this hypothesis in a long-lived mammal, the roe deer, using data from two contrasting populations, intensively monitored for more than 35 years. In the highly productive site, the fitness of female roe deer increased with the quality of environment during adulthood and, contrary to predictions of PAR, individuals born in good conditions always outperformed those born under poor conditions. In the resource-limited site, the fitness of female roe deer born in poor years was better than those born in good conditions in poor years when the animals were adult, but not in good years. Although consistent with predictions of PAR, we showed that this pattern is likely to be a consequence of increased viability selection during the juvenile stage for animals born in poor years. While PARs are often advanced in evolutionary medicine, our findings suggest that detailed biological processes should be investigated before drawing conclusions about the existence of this phenomenon.}, + number = {1785}, + urldate = {2024-09-04}, + journal = {Proceedings of the Royal Society B: Biological Sciences}, + author = {Douhard, Mathieu and Plard, Floriane and Gaillard, Jean-Michel and Capron, Gilles and Delorme, Daniel and Klein, François and Duncan, Patrick and Loe, Leif Egil and Bonenfant, Christophe}, + month = jun, + year = {2014}, + note = {Publisher: Royal Society}, + keywords = {phenotypic plasticity, development, adaptation, long-term cohort effects, silver spoon effect}, + pages = {20140276}, + file = {Full Text PDF:/Users/emiliobruna/Zotero/storage/AMW6UMBB/Douhard et al. - 2014 - Fitness consequences of environmental conditions a.pdf:application/pdf}, +} + +@article{riveroDelayedLeafSenescence2007, + title = {Delayed leaf senescence induces extreme drought tolerance in a flowering plant}, + volume = {104}, + url = {https://www.pnas.org/doi/abs/10.1073/pnas.0709453104}, + doi = {10.1073/pnas.0709453104}, + abstract = {Drought, the most prominent threat to agricultural production worldwide, accelerates leaf senescence, leading to a decrease in canopy size, loss in photosynthesis and reduced yields. On the basis of the assumption that senescence is a type of cell death program that could be inappropriately activated during drought, we hypothesized that it may be possible to enhance drought tolerance by delaying drought-induced leaf senescence. We generated transgenic plants expressing an isopentenyltransferase gene driven by a stress- and maturation-induced promoter. Remarkably, the suppression of drought-induced leaf senescence resulted in outstanding drought tolerance as shown by, among other responses, vigorous growth after a long drought period that killed the control plants. The transgenic plants maintained high water contents and retained photosynthetic activity (albeit at a reduced level) during the drought. Moreover, the transgenic plants displayed minimal yield loss when watered with only 30\% of the amount of water used under control conditions. The production of drought-tolerant crops able to grow under restricted water regimes without diminution of yield would minimize drought-related losses and ensure food production in water-limited lands.}, + number = {49}, + urldate = {2024-09-04}, + journal = {Proceedings of the National Academy of Sciences}, + author = {Rivero, Rosa M. and Kojima, Mikiko and Gepstein, Amira and Sakakibara, Hitoshi and Mittler, Ron and Gepstein, Shimon and Blumwald, Eduardo}, + month = dec, + year = {2007}, + note = {Publisher: Proceedings of the National Academy of Sciences}, + pages = {19631--19636}, + file = {Full Text PDF:/Users/emiliobruna/Zotero/storage/VJ7FF4UH/Rivero et al. - 2007 - Delayed leaf senescence induces extreme drought to.pdf:application/pdf}, +} + +@article{simaoDevelopmentalAnatomyMorphology2005, + title = {Developmental {Anatomy} and {Morphology} of the {Ovule} and {Seed} of {Heliconia} ({Heliconiaceae}, {Zingiberales})}, + volume = {8}, + copyright = {Georg Thieme Verlag Stuttgart KG · New York}, + issn = {1435-8603}, + url = {https://www.thieme-connect.com/products/ejournals/html/10.1055/s-2005-872815}, + doi = {10.1055/s-2005-872815}, + abstract = {Thieme E-Books \& E-Journals}, + language = {en}, + urldate = {2024-09-04}, + journal = {Plant Biology}, + author = {Simão, D. G. and Scatena, V. L. and Bouman, F.}, + month = dec, + year = {2005}, + note = {Publisher: Georg Thieme Verlag Stuttgart KG · New York}, + keywords = {Heliconia, Zingiberales, \# +Key words +Embryo, megagametogenesis, megasporogenesis, pyrene}, + pages = {143--154}, + file = {Full Text PDF:/Users/emiliobruna/Zotero/storage/77UNNY8D/Simão et al. - 2005 - Developmental Anatomy and Morphology of the Ovule .pdf:application/pdf}, +} + +@article{eversLaggedDormantSeason2021a, + title = {Lagged and dormant season climate better predict plant vital rates than climate during the growing season}, + volume = {27}, + copyright = {© 2021 The Authors. Global Change Biology published by John Wiley \& Sons Ltd}, + issn = {1365-2486}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.15519}, + doi = {10.1111/gcb.15519}, + abstract = {Understanding the effects of climate on the vital rates (e.g., survival, development, reproduction) and dynamics of natural populations is a long-standing quest in ecology, with ever-increasing relevance in the face of climate change. However, linking climate drivers to demographic processes requires identifying the appropriate time windows during which climate influences vital rates. Researchers often do not have access to the long-term data required to test a large number of windows, and are thus forced to make a priori choices. In this study, we first synthesize the literature to assess current a priori choices employed in studies performed on 104 plant species that link climate drivers with demographic responses. Second, we use a sliding-window approach to investigate which combination of climate drivers and temporal window have the best predictive ability for vital rates of four perennial plant species that each have over a decade of demographic data (Helianthella quinquenervis, Frasera speciosa, Cylindriopuntia imbricata, and Cryptantha flava). Our literature review shows that most studies consider time windows in only the year preceding the measurement of the vital rate(s) of interest, and focus on annual or growing season temporal scales. In contrast, our sliding-window analysis shows that in only four out of 13 vital rates the selected climate drivers have time windows that align with, or are similar to, the growing season. For many vital rates, the best window lagged more than 1 year and up to 4 years before the measurement of the vital rate. Our results demonstrate that for the vital rates of these four species, climate drivers that are lagged or outside of the growing season are the norm. Our study suggests that considering climatic predictors that fall outside of the most recent growing season will improve our understanding of how climate affects population dynamics.}, + language = {en}, + number = {9}, + urldate = {2024-09-04}, + journal = {Global Change Biology}, + author = {Evers, Sanne M. and Knight, Tiffany M. and Inouye, David W. and Miller, Tom E. X. and Salguero-Gómez, Roberto and Iler, Amy M. and Compagnoni, Aldo}, + year = {2021}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/gcb.15519}, + keywords = {plant demography, precipitation, temperature, sliding window, carryover effects, environmental driver, lagged effects}, + pages = {1927--1941}, + file = {Full Text PDF:/Users/emiliobruna/Zotero/storage/IVGN2LLT/Evers et al. - 2021 - Lagged and dormant season climate better predict p.pdf:application/pdf;Snapshot:/Users/emiliobruna/Zotero/storage/FDES4IIV/gcb.html:text/html}, +} + +@article{bradshawLightTimePhysiology2010, + title = {Light, {Time}, and the {Physiology} of {Biotic} {Response} to {Rapid} {Climate} {Change} in {Animals}}, + volume = {72}, + issn = {0066-4278, 1545-1585}, + url = {https://www.annualreviews.org/content/journals/10.1146/annurev-physiol-021909-135837}, + doi = {10.1146/annurev-physiol-021909-135837}, + abstract = {Examination of temperate and polar regions of Earth shows that the nonbiological world is exquisitely sensitive to the direct effects of temperature, whereas the biological world is largely organized by light. Herein, we discuss the use of day length by animals at physiological and genetic levels, beginning with a comparative experimental study that shows the preeminent role of light in determining fitness in seasonal environments. Typically, at seasonally appropriate times, light initiates a cascade of physiological events mediating the input and interpretation of day length to the output of specific hormones that ultimately determine whether animals prepare to develop, reproduce, hibernate, enter dormancy, or migrate. The mechanisms that form the basis of seasonal time keeping and their adjustment during climate change are reviewed at the physiological and genetic levels. Future avenues for research are proposed that span basic questions from how animals transition from dependency on tropical cues to temperate cues during range expansions, to more applied questions of species survival and conservation biology during periods of climatic stress.}, + language = {en}, + number = {Volume 72, 2010}, + urldate = {2024-11-07}, + journal = {Annual Review of Physiology}, + author = {Bradshaw, William E. and Holzapfel, Christina M.}, + month = mar, + year = {2010}, + note = {Publisher: Annual Reviews}, + pages = {147--166}, + file = {Snapshot:/Users/emiliobruna/Zotero/storage/KB326B9Q/annurev-physiol-021909-135837.html:text/html}, +} + +@article{bradshawLightTimePhysiology2010a, + title = {Light, {Time}, and the {Physiology} of {Biotic} {Response} to {Rapid} {Climate} {Change} in {Animals}}, + volume = {72}, + issn = {0066-4278, 1545-1585}, + url = {https://www.annualreviews.org/doi/10.1146/annurev-physiol-021909-135837}, + doi = {10.1146/annurev-physiol-021909-135837}, + abstract = {Examination of temperate and polar regions of Earth shows that the nonbiological world is exquisitely sensitive to the direct effects of temperature, whereas the biological world is largely organized by light. Herein, we discuss the use of day length by animals at physiological and genetic levels, beginning with a comparative experimental study that shows the preeminent role of light in determining fitness in seasonal environments. Typically, at seasonally appropriate times, light initiates a cascade of physiological events mediating the input and interpretation of day length to the output of specific hormones that ultimately determine whether animals prepare to develop, reproduce, hibernate, enter dormancy, or migrate. The mechanisms that form the basis of seasonal time keeping and their adjustment during climate change are reviewed at the physiological and genetic levels. Future avenues for research are proposed that span basic questions from how animals transition from dependency on tropical cues to temperate cues during range expansions, to more applied questions of species survival and conservation biology during periods of climatic stress.}, + language = {en}, + number = {1}, + urldate = {2024-11-07}, + journal = {Annual Review of Physiology}, + author = {Bradshaw, William E. and Holzapfel, Christina M.}, + month = mar, + year = {2010}, + pages = {147--166}, + file = {PDF:/Users/emiliobruna/Zotero/storage/JTK7ZVBA/Bradshaw and Holzapfel - 2010 - Light, Time, and the Physiology of Biotic Response to Rapid Climate Change in Animals.pdf:application/pdf}, +} + +@article{wellsEnvironmentalEffectsIndividual2016, + title = {Environmental effects and individual body condition drive seasonal fecundity of rabbits: identifying acute and lagged processes}, + volume = {181}, + issn = {1432-1939}, + shorttitle = {Environmental effects and individual body condition drive seasonal fecundity of rabbits}, + url = {https://doi.org/10.1007/s00442-016-3617-2}, + doi = {10.1007/s00442-016-3617-2}, + abstract = {The reproduction of many species is determined by seasonally-driven resource supply. But it is difficult to quantify whether the fecundity is sensitive to short- or long-term exposure to environmental conditions such as rainfall that drive resource supply. Using 25 years of data on individual fecundity of European female rabbits, Oryctolagus cuniculus, from semiarid Australia, we investigate the role of individual body condition, rainfall and temperature as drivers of seasonal and long-term and population-level changes in fecundity (breeding probability, ovulation rate, embryo survival). We built distributed lag models in a hierarchical Bayesian framework to account for both immediate and time-lagged effects of climate and other environmental drivers, and possible shifts in reproduction over consecutive seasons. We show that rainfall during summer, when rabbits typically breed only rarely, increased breeding probability immediately and with time lags of up to 10 weeks. However, an earlier onset of the yearly breeding period did not result in more overall reproductive output. Better body condition was associated with an earlier onset of breeding and higher embryo survival. Breeding probability in the main breeding season declined with increased breeding activity in the preceding season and only individuals in good body condition were able to breed late in the season. Higher temperatures reduce breeding success across seasons. We conclude that a better understanding of seasonal dynamics and plasticity (and their interplay) in reproduction will provide crucial insights into how lagomorphs are likely to respond and potentially adapt to the influence of future climate and other environmental change.}, + language = {en}, + number = {3}, + urldate = {2024-11-07}, + journal = {Oecologia}, + author = {Wells, Konstans and O’Hara, Robert B. and Cooke, Brian D. and Mutze, Greg J. and Prowse, Thomas A. A. and Fordham, Damien A.}, + month = jul, + year = {2016}, + keywords = {Dynamic optimization, Invasive species, Lagged effects, Reproduction, Seasonality}, + pages = {853--864}, + file = {Full Text PDF:/Users/emiliobruna/Zotero/storage/XCV5IAFG/Wells et al. - 2016 - Environmental effects and individual body condition drive seasonal fecundity of rabbits identifying.pdf:application/pdf}, +} + +@article{kussEvolutionaryDemographyLonglived2008a, + title = {Evolutionary demography of long-lived monocarpic perennials: a time-lagged integral projection model}, + volume = {96}, + copyright = {© 2008 The Authors. Journal compilation © 2008 British Ecological Society}, + issn = {1365-2745}, + shorttitle = {Evolutionary demography of long-lived monocarpic perennials}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2745.2008.01374.x}, + doi = {10.1111/j.1365-2745.2008.01374.x}, + abstract = {1 The evolution of flowering strategies (when and at what size to flower) in monocarpic perennials is determined by balancing current reproduction with expected future reproduction, and these are largely determined by size-specific patterns of growth and survival. However, because of the difficulty in following long-lived individuals throughout their lives, this theory has largely been tested using short-lived species ({\textless} 5 years). 2 Here, we tested this theory using the long-lived monocarpic perennial Campanula thyrsoides which can live up to 16 years. We used a novel approach that combined permanent plot and herb chronology data from a 3-year field study to parameterize and validate integral projection models (IPMs). 3 Similar to other monocarpic species, the rosette leaves of C. thyrsoides wither over winter and so size cannot be measured in the year of flowering. We therefore extended the existing IPM framework to incorporate an additional time delay that arises because flowering demography must be predicted from rosette size in the year before flowering. 4 We found that all main demographic functions (growth, survival probability, flowering probability and fecundity) were strongly size-dependent and there was a pronounced threshold size of flowering. There was good agreement between the predicted distribution of flowering ages obtained from the IPMs and that estimated in the field. Mostly, there was good agreement between the IPM predictions and the direct quantitative field measurements regarding the demographic parameters λ, R0 and T. We therefore conclude that the model captures the main demographic features of the field populations. 5 Elasticity analysis indicated that changes in the survival and growth function had the largest effect (c. 80\%) on λ and this was considerably larger than in short-lived monocarps. We found only weak selection pressure operating on the observed flowering strategy which was close to the predicted evolutionary stable strategy. 6 Synthesis. The extended IPM accurately described the demography of a long-lived monocarpic perennial using data collected over a relatively short period. We could show that the evolution of flowering strategies in short- and long-lived monocarps seem to follow the same general rules but with a longevity-related emphasis on survival over fecundity.}, + language = {en}, + number = {4}, + urldate = {2024-11-07}, + journal = {Journal of Ecology}, + author = {Kuss, Patrick and Rees, Mark and Ægisdóttir, Hafdís Hanna and Ellner, Stephen P. and Stöcklin, Jürg}, + year = {2008}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2745.2008.01374.x}, + keywords = {alpine plants, Campanula thyrsoides, elasticity analysis, European Alps, evolutionary stable strategy, flowering threshold, life-history evolution, semelparity, size-structured populations, stable size distribution}, + pages = {821--832}, + file = {Full Text PDF:/Users/emiliobruna/Zotero/storage/4HRWB7BF/Kuss et al. - 2008 - Evolutionary demography of long-lived monocarpic perennials a time-lagged integral projection model.pdf:application/pdf;Snapshot:/Users/emiliobruna/Zotero/storage/K8QZHQWS/j.1365-2745.2008.01374.html:text/html}, +} + +@article{brothertonImmediateLagEffects2019, + title = {Immediate and lag effects of hydrological change on floodplain grassland plants}, + volume = {220}, + issn = {1573-5052}, + url = {https://doi.org/10.1007/s11258-019-00918-z}, + doi = {10.1007/s11258-019-00918-z}, + abstract = {Hydrological alteration due to climate change events such as floods and drought is a significant threat to globally important wetlands, including floodplain wet grasslands. This research incorporated two field experiments with the aim to assess immediate and longer-term functional responses of floodplain plants to hydrological change. Plant introductions and transplants between a wetter riparian and a drier site in southern England were used to simulate hydrological change. Species showed immediate and differential responses to contrasting hydrologies. Rhinanthus minor, a hemi-parasitic annual species with ruderal traits, was lost from the riparian grassland within four weeks. The survival and production of a leguminous perennial, Lathyrus pratensis, in high groundwater levels soon decreased. However, the perennial Primula veris mostly functioned well in contrasting hydrological regimes, possibly because it can tolerate stress. The perennial wetland species Caltha palustris showed lag effects, over three years, when its hydrology was altered to a sub-optimal drier scenario by transplantation, with declining survival and a sustained reduction in leaf production and flowering. Disturbance caused by transplantation and weather conditions also affected its performance. Thus, this study shows that some functionally important floodplain species may succumb within weeks to a hydrological event facilitated by climate change, unless they are able to tolerate the challenging conditions, while the performance of other characteristic species could decline and continue to show constrained performance for years as a consequence of altered hydrology.}, + language = {en}, + number = {3}, + urldate = {2024-11-07}, + journal = {Plant Ecology}, + author = {Brotherton, Sarah J. and Joyce, Chris B. and Berg, Maureen J. and Awcock, Graeme J.}, + month = mar, + year = {2019}, + keywords = {Climate change, Flowering, Plant traits, Production, Survival, Wetlands}, + pages = {345--359}, + file = {Full Text PDF:/Users/emiliobruna/Zotero/storage/HWCHJ27Y/Brotherton et al. - 2019 - Immediate and lag effects of hydrological change on floodplain grassland plants.pdf:application/pdf}, +} + +@article{tenhumbergTimelaggedEffectsWeather2018a, + title = {Time-lagged effects of weather on plant demography: drought and {Astragalus} scaphoides}, + volume = {99}, + copyright = {© 2018 The Authors Ecology published by Wiley Periodicals, Inc. on behalf of Ecological Society of America.}, + issn = {1939-9170}, + shorttitle = {Time-lagged effects of weather on plant demography}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ecy.2163}, + doi = {10.1002/ecy.2163}, + abstract = {Temperature and precipitation determine the conditions where plant species can occur. Despite their significance, to date, surprisingly few demographic field studies have considered the effects of abiotic drivers. This is problematic because anticipating the effect of global climate change on plant population viability requires understanding how weather variables affect population dynamics. One possible reason for omitting the effect of weather variables in demographic studies is the difficulty in detecting tight associations between vital rates and environmental drivers. In this paper, we applied Functional Linear Models (FLMs) to long-term demographic data of the perennial wildflower, Astragalus scaphoides, and explored sensitivity of the results to reduced amounts of data. We compared models of the effect of average temperature, total precipitation, or an integrated measure of drought intensity (standardized precipitation evapotranspiration index, SPEI), on plant vital rates. We found that transitions to flowering and recruitment in year t were highest if winter/spring of year t was wet (positive effect of SPEI). Counterintuitively, if the preceding spring of year t − 1 was wet, flowering probabilities were decreased (negative effect of SPEI). Survival of vegetative plants from t − 1 to t was also negatively affected by wet weather in the spring of year t − 1 and, for large plants, even wet weather in the spring of t − 2 had a negative effect. We assessed the integrated effect of all vital rates on life history performance by fitting FLMs to the asymptotic growth rate, log(). Log() was highest if dry conditions in year t − 1 were followed by wet conditions in the year t. Overall, the positive effects of wet years exceeded their negative effects, suggesting that increasing frequency of drought conditions would reduce population viability of A. scaphoides. The drought signal weakened when reducing the number of monitoring years. Substituting space for time did not recover the weather signal, probably because the weather variables varied little between sites. We detected the SPEI signal when the analysis included data from two sites monitored over 20 yr (2 × 20 observations), but not when analyzing data from four sites monitored over 10 yr (4 × 10 observations).}, + language = {en}, + number = {4}, + urldate = {2024-11-07}, + journal = {Ecology}, + author = {Tenhumberg, Brigitte and Crone, Elizabeth E. and Ramula, Satu and Tyre, Andrew J.}, + year = {2018}, + note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ecy.2163}, + keywords = {carryover effects, detecting weather signals, drought, environmental drivers, matrix models, plant demography, space for time substitution}, + pages = {915--925}, + file = {Full Text PDF:/Users/emiliobruna/Zotero/storage/BEEF8XNA/Tenhumberg et al. - 2018 - Time-lagged effects of weather on plant demography drought and Astragalus scaphoides.pdf:application/pdf;Snapshot:/Users/emiliobruna/Zotero/storage/634V9LHS/ecy.html:text/html}, +} + +@article{reynoldsDelayedInducedSilica2012, + title = {Delayed induced silica defences in grasses and their potential for destabilising herbivore population dynamics}, + volume = {170}, + issn = {1432-1939}, + url = {https://doi.org/10.1007/s00442-012-2326-8}, + doi = {10.1007/s00442-012-2326-8}, + abstract = {Some grass species mount a defensive response to grazing by increasing their rate of uptake of silica from the soil and depositing it as abrasive granules in their leaves. Increased plant silica levels reduce food quality for herbivores that feed on these grasses. Here we provide empirical evidence that a principal food species of an herbivorous rodent exhibits a delayed defensive response to grazing by increasing silica concentrations, and present theoretical modelling that predicts that such a response alone could lead to the population cycles observed in some herbivore populations. Experiments performed under greenhouse conditions revealed that the rate of deposition of silica defences in the grass Deschampsia caespitosa is a time-lagged, nonlinear function of grazing intensity and that, upon cessation of grazing, these defences take around one year to decay to within 5 \% of control levels. Simple coupled grass–herbivore population models incorporating this functional response, and parameterised with empirical data, consistently predict population cycles for a wide range of realistic parameter values for a (Microtus) vole–grass system. Our results support the hypothesis that induced silica defences have the potential to strongly affect the population dynamics of their herbivores. Specifically, the feedback response we observed could be a driving mechanism behind the observed population cycles in graminivorous herbivores in cases where grazing levels in the field become sufficiently large and sustained to trigger an induced silica defence response.}, + language = {en}, + number = {2}, + urldate = {2024-11-07}, + journal = {Oecologia}, + author = {Reynolds, Jennifer J. H. and Lambin, Xavier and Massey, Fergus P. and Reidinger, Stefan and Sherratt, Jonathan A. and Smith, Matthew J. and White, Andrew and Hartley, Sue E.}, + month = oct, + year = {2012}, + keywords = {Functional response, Herbivory, Population cycles, Trophic interactions, Voles}, + pages = {445--456}, + file = {Full Text PDF:/Users/emiliobruna/Zotero/storage/ENUT48NX/Reynolds et al. - 2012 - Delayed induced silica defences in grasses and their potential for destabilising herbivore populatio.pdf:application/pdf}, +} diff --git a/docs/templates/the-american-naturalist.csl b/docs/templates/the-american-naturalist.csl index c8bff84..3b6fb8c 100644 --- a/docs/templates/the-american-naturalist.csl +++ b/docs/templates/the-american-naturalist.csl @@ -311,7 +311,7 @@ - +