1

I am using apalike bibliography in an article but for some reason, certain citations end up exceeding the margins of the page. In some paragraphs, the citations are formatted correctly, e.g. paragraphs 1 and 3. But I cannot seem to be able to fix the issue in the second paragraph.

EDIT: I believe this caused by the parskip package I used to not indent my paragraphs. Is there a way to not have this issue using this package?

\documentclass[11pt]{article}
\usepackage[margin=2cm]{geometry}
\usepackage{parskip}
\usepackage{setspace}
\doublespacing


\begin{document}
\section{Introduction}

\subsection{Background}
It was long believed that studying natural evolution would require time scales exceeding the lifespan of any researcher. Darwin himself felt that directly observing evolution was not possible and relied on comparing phenotypic similarities between fossilized ancestral remains \cite{darwin1876origin}. His pioneering theory of evolution focused on larger eukaryotic species, and his methods are still of great importance today when used alongside newer techniques such as DNA and protein sequencing \cite{gallone2016domestication,hug2016new,gubry2015coupling}.

However, since then, researchers have learned that microorganisms, such as bacteria, fungi, and viruses, display much more rapid evolutionary changes. This makes them incredibly practical for experimenting with and monitoring evolution in controlled enviornments \cite{de1892experimental, dallinger1878life,van2018experimental}.  They replicate quickly, have very simple requirements for growth and are also very small meaning that their populations can be experimented on cheaply and easily for many generations in a short amount of time. Experiments can also be repeated and restarted at any given point in time with differing initial conditions. 

Most importantly of all, the study of evolution in microorganisms specifically is extremely important for many reasons. Microorganisms are often disease causing pathogens and are responsible for many illnesses. Their short generation times allow them to rapidly acquire resistances to harmful stimuli in the environment by means of evolution, and these harmful stimuli include treatment methods such as antibiotics. Finding methods to control and overcome resistance evolution in microorganisms, particularly bacteria, is therefore critical to the advancement of modern medicine \cite{ling2015new,durao2018evolutionary, baym2016multidrug}. 


\bibliographystyle{apalike} 
\bibliography{bibliography}
\end{document}

enter image description here

bibliography.bib file:

@article{krishna2007uv,
  title={UV-induced mutagenesis in Escherichia coli SOS response: a quantitative model},
  author={Krishna, Sandeep and Maslov, Sergei and Sneppen, Kim},
  journal={PLoS Comput Biol},
  volume={3},
  number={3},
  pages={e41},
  year={2007},
  publisher={Public Library of Science}
}

@book{darwin1876origin,
    title={The origin of species by means of natural selection, or, the preservation of favoured races in the struggle for life},
    author={Darwin, Charles},
    year={1876},
    publisher={John murray}
}
@article{gallone2016domestication,
    title={Domestication and divergence of Saccharomyces cerevisiae beer yeasts},
    author={Gallone, Brigida and Steensels, Jan and Prahl, Troels and Soriaga, Leah and Saels, Veerle and Herrera-Malaver, Beatriz and Merlevede, Adriaan and Roncoroni, Miguel and Voordeckers, Karin and Miraglia, Loren and others},
    journal={Cell},
    volume={166},
    number={6},
    pages={1397--1410},
    year={2016},
    publisher={Elsevier}
}
@article{hug2016new,
    title={A new view of the tree of life},
    author={Hug, Laura A and Baker, Brett J and Anantharaman, Karthik and Brown, Christopher T and Probst, Alexander J and Castelle, Cindy J and Butterfield, Cristina N and Hernsdorf, Alex W and Amano, Yuki and Ise, Kotaro and others},
    journal={Nature microbiology},
    volume={1},
    number={5},
    pages={1--6},
    year={2016},
    publisher={Nature Publishing Group}
}

@article{gubry2015coupling,
    title={Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota},
    author={Gubry-Rangin, C{\'e}cile and Kratsch, Christina and Williams, Tom A and McHardy, Alice C and Embley, T Martin and Prosser, James I and Macqueen, Daniel J},
    journal={Proceedings of the National Academy of Sciences},
    volume={112},
    number={30},
    pages={9370--9375},
    year={2015},
    publisher={National Acad Sciences}
}
@book{de1892experimental,
    title={Experimental Evolution: Lectures Delivered in the" Summer School of Art and Science", University Hall, Edinburgh (August, 1891)},
    author={De Varigny, Henry},
    year={1892},
    publisher={Macmillan and Company}
}
@article{woese1987bacterial,
    title={Bacterial evolution.},
    author={Woese, Carl R},
    journal={Microbiological reviews},
    volume={51},
    number={2},
    pages={221},
    year={1987},
    publisher={American Society for Microbiology (ASM)}
}

@article{dallinger1878life,
    title={I. On the life-history of a minute septic organisms with an account of experiments made to determine its thermal death point},
    author={Dallinger, William Henry},
    journal={Proceedings of the Royal Society of London},
    volume={27},
    number={185-189},
    pages={332--350},
    year={1878},
    publisher={The Royal Society London}
}

@article{ling2015new,
    title={A new antibiotic kills pathogens without detectable resistance},
    author={Ling, Losee L and Schneider, Tanja and Peoples, Aaron J and Spoering, Amy L and Engels, Ina and Conlon, Brian P and Mueller, Anna and Sch{\"a}berle, Till F and Hughes, Dallas E and Epstein, Slava and others},
    journal={Nature},
    volume={517},
    number={7535},
    pages={455--459},
    year={2015},
    publisher={Nature Publishing Group}
}
@article{durao2018evolutionary,
    title={Evolutionary mechanisms shaping the maintenance of antibiotic resistance},
    author={Dur{\~a}o, Paulo and Balbont{\'\i}n, Roberto and Gordo, Isabel},
    journal={Trends in microbiology},
    volume={26},
    number={8},
    pages={677--691},
    year={2018},
    publisher={Elsevier}
}
@article{baym2016multidrug,
    title={Multidrug evolutionary strategies to reverse antibiotic resistance},
    author={Baym, Michael and Stone, Laura K and Kishony, Roy},
    journal={Science},
    volume={351},
    number={6268},
    year={2016},
    publisher={American Association for the Advancement of Science}
}
@article{van2018experimental,
    title={Experimental design, population dynamics, and diversity in microbial experimental evolution},
    author={Van den Bergh, Bram and Swings, Toon and Fauvart, Maarten and Michiels, Jan},
    journal={Microbiology and Molecular Biology Reviews},
    volume={82},
    number={3},
    year={2018},
    publisher={Am Soc Microbiol}
}
@article{kimura1989neutral,
    title={The neutral theory of molecular evolution and the world view of the neutralists},
    author={Kimura, Motoo},
    journal={Genome},
    volume={31},
    number={1},
    pages={24--31},
    year={1989},
    publisher={NRC Research Press Ottawa, Canada}
}

@article{pal2015collateral,
    title={Collateral sensitivity of antibiotic-resistant microbes},
    author={P{\'a}l, Csaba and Papp, Bal{\'a}zs and L{\'a}z{\'a}r, Vikt{\'o}ria},
    journal={Trends in microbiology},
    volume={23},
    number={7},
    pages={401--407},
    year={2015},
    publisher={Elsevier}
}
@article{shibai2017mutation,
    title={Mutation accumulation under UV radiation in Escherichia coli},
    author={Shibai, Atsushi and Takahashi, Yusuke and Ishizawa, Yuka and Motooka, Daisuke and Nakamura, Shota and Ying, Bei-Wen and Tsuru, Saburo},
    journal={Scientific reports},
    volume={7},
    number={1},
    pages={1--12},
    year={2017},
    publisher={Nature Publishing Group}
}

@article{taddei1997role,
    title={Role of mutator alleles in adaptive evolution},
    author={Taddei, Fran{\c{c}}ois and Radman, Miroslav and Maynard-Smith, John and Toupance, Bruno and Gouyon, Pierre-Henri and Godelle, Bernard},
    journal={Nature},
    volume={387},
    number={6634},
    pages={700--702},
    year={1997},
    publisher={Nature Publishing Group}
}
2
  • Please add the .bib file with the references you are using in your MWE. May 7 at 21:01
  • I have added the .bib file
    – Chryron
    May 7 at 21:23
2

The issue you're encountering is not caused by the use of the parskip package.

The apalike bibliography style requires the use of a suitable citation management package, say, the natbib package:

\usepackage[round]{natbib}

Another good reason for employing the natbib package is that it's perfectly interoperable with the hyperref package.

If you go with the natbib package, I'd also replace the 4 instances of \cite with \citep, to create parenthesis-style citation call-outs.

Finally, don't forget to encase words such as Saccharomyces in the title fields in curly braces, to prevent BibTeX from rendering them in all-lowercase.

enter image description here

\documentclass[11pt]{article}
\begin{filecontents}[overwrite]{mybib.bib}  % create a test bib file "on the fly"
@article{krishna2007uv,
  title={UV-induced mutagenesis in Escherichia coli SOS response: a quantitative model},
  author={Krishna, Sandeep and Maslov, Sergei and Sneppen, Kim},
  journal={PLoS Comput Biol},
  volume={3},
  number={3},
  pages={e41},
  year={2007},
  publisher={Public Library of Science}
}

@book{darwin1876origin,
    title={The origin of species by means of natural selection, or, the preservation of favoured races in the struggle for life},
    author={Darwin, Charles},
    year={1876},
    publisher={John murray}
}
@article{gallone2016domestication,
    title={Domestication and divergence of {Saccharomyces} cerevisiae beer yeasts},
    author={Gallone, Brigida and Steensels, Jan and Prahl, Troels and Soriaga, Leah and Saels, Veerle and Herrera-Malaver, Beatriz and Merlevede, Adriaan and Roncoroni, Miguel and Voordeckers, Karin and Miraglia, Loren and others},
    journal={Cell},
    volume={166},
    number={6},
    pages={1397--1410},
    year={2016},
    publisher={Elsevier}
}
@article{hug2016new,
    title={A new view of the tree of life},
    author={Hug, Laura A and Baker, Brett J and Anantharaman, Karthik and Brown, Christopher T and Probst, Alexander J and Castelle, Cindy J and Butterfield, Cristina N and Hernsdorf, Alex W and Amano, Yuki and Ise, Kotaro and others},
    journal={Nature microbiology},
    volume={1},
    number={5},
    pages={1--6},
    year={2016},
    publisher={Nature Publishing Group}
}

@article{gubry2015coupling,
    title={Coupling of diversification and pH adaptation during the evolution of terrestrial {Thaumarchaeota}},
    author={Gubry-Rangin, C{\'e}cile and Kratsch, Christina and Williams, Tom A and McHardy, Alice C and Embley, T Martin and Prosser, James I and Macqueen, Daniel J},
    journal={Proceedings of the National Academy of Sciences},
    volume={112},
    number={30},
    pages={9370--9375},
    year={2015},
    publisher={National Acad Sciences}
}
@book{de1892experimental,
    title={Experimental Evolution: Lectures Delivered in the ``{Summer School of Art and Science}'', {University Hall, Edinburgh (August, 1891)}},
    author={De Varigny, Henry},
    year={1892},
    publisher={Macmillan and Company}
}
@article{woese1987bacterial,
    title={Bacterial evolution},
    author={Woese, Carl R},
    journal={Microbiological reviews},
    volume={51},
    number={2},
    pages={221},
    year={1987},
    publisher={American Society for Microbiology (ASM)}
}

@article{dallinger1878life,
    title={I. {On} the life-history of a minute septic organisms with an account of experiments made to determine its thermal death point},
    author={Dallinger, William Henry},
    journal={Proceedings of the Royal Society of London},
    volume={27},
    number={185-189},
    pages={332--350},
    year={1878},
    publisher={The Royal Society London}
}

@article{ling2015new,
    title={A new antibiotic kills pathogens without detectable resistance},
    author={Ling, Losee L and Schneider, Tanja and Peoples, Aaron J and Spoering, Amy L and Engels, Ina and Conlon, Brian P and Mueller, Anna and Sch{\"a}berle, Till F and Hughes, Dallas E and Epstein, Slava and others},
    journal={Nature},
    volume={517},
    number={7535},
    pages={455--459},
    year={2015},
    publisher={Nature Publishing Group}
}
@article{durao2018evolutionary,
    title={Evolutionary mechanisms shaping the maintenance of antibiotic resistance},
    author={Dur{\~a}o, Paulo and Balbont{\'\i}n, Roberto and Gordo, Isabel},
    journal={Trends in microbiology},
    volume={26},
    number={8},
    pages={677--691},
    year={2018},
    publisher={Elsevier}
}
@article{baym2016multidrug,
    title={Multidrug evolutionary strategies to reverse antibiotic resistance},
    author={Baym, Michael and Stone, Laura K and Kishony, Roy},
    journal={Science},
    volume={351},
    number={6268},
    year={2016},
    publisher={American Association for the Advancement of Science}
}
@article{van2018experimental,
    title={Experimental design, population dynamics, and diversity in microbial experimental evolution},
    author={Van den Bergh, Bram and Swings, Toon and Fauvart, Maarten and Michiels, Jan},
    journal={Microbiology and Molecular Biology Reviews},
    volume={82},
    number={3},
    year={2018},
    publisher={Am Soc Microbiol}
}
@article{kimura1989neutral,
    title={The neutral theory of molecular evolution and the world view of the neutralists},
    author={Kimura, Motoo},
    journal={Genome},
    volume={31},
    number={1},
    pages={24--31},
    year={1989},
    publisher={NRC Research Press Ottawa, Canada}
}

@article{pal2015collateral,
    title={Collateral sensitivity of antibiotic-resistant microbes},
    author={P{\'a}l, Csaba and Papp, Bal{\'a}zs and L{\'a}z{\'a}r, Vikt{\'o}ria},
    journal={Trends in microbiology},
    volume={23},
    number={7},
    pages={401--407},
    year={2015},
    publisher={Elsevier}
}
@article{shibai2017mutation,
    title={Mutation accumulation under UV radiation in Escherichia coli},
    author={Shibai, Atsushi and Takahashi, Yusuke and Ishizawa, Yuka and Motooka, Daisuke and Nakamura, Shota and Ying, Bei-Wen and Tsuru, Saburo},
    journal={Scientific reports},
    volume={7},
    number={1},
    pages={1--12},
    year={2017},
    publisher={Nature Publishing Group}
}

@article{taddei1997role,
    title={Role of mutator alleles in adaptive evolution},
    author={Taddei, Fran{\c{c}}ois and Radman, Miroslav and Maynard-Smith, John and Toupance, Bruno and Gouyon, Pierre-Henri and Godelle, Bernard},
    journal={Nature},
    volume={387},
    number={6634},
    pages={700--702},
    year={1997},
    publisher={Nature Publishing Group}
}
\end{filecontents}

\usepackage[margin=2cm]{geometry}
\usepackage{parskip}
\usepackage{setspace}
%\doublespacing % not needed for this example

\usepackage[round]{natbib}
\bibliographystyle{apalike} 
\usepackage[colorlinks,allcolors=blue]{hyperref} % optional

\begin{document}
\section{Introduction}

\subsection{Background}
It was long believed that studying natural evolution would require time scales exceeding the lifespan of any researcher. Darwin himself felt that directly observing evolution was not possible and relied on comparing phenotypic similarities between fossilized ancestral remains \citep{darwin1876origin}. His pioneering theory of evolution focused on larger eukaryotic species, and his methods are still of great importance today when used alongside newer techniques such as DNA and protein sequencing \citep{gallone2016domestication,hug2016new,gubry2015coupling}.

However, since then, researchers have learned that microorganisms, such as bacteria, fungi, and viruses, display much more rapid evolutionary changes. This makes them incredibly practical for experimenting with and monitoring evolution in controlled enviornments \citep{de1892experimental, dallinger1878life,van2018experimental}.  They replicate quickly, have very simple requirements for growth and are also very small meaning that their populations can be experimented on cheaply and easily for many generations in a short amount of time. Experiments can also be repeated and restarted at any given point in time with differing initial conditions. 

Most importantly of all, the study of evolution in microorganisms specifically is extremely important for many reasons. Microorganisms are often disease causing pathogens and are responsible for many illnesses. Their short generation times allow them to rapidly acquire resistances to harmful stimuli in the environment by means of evolution, and these harmful stimuli include treatment methods such as antibiotics. Finding methods to control and overcome resistance evolution in microorganisms, particularly bacteria, is therefore critical to the advancement of modern medicine \citep{ling2015new,durao2018evolutionary, baym2016multidrug}. 

\bibliography{mybib}
\end{document}
1
  • thank you for the help!
    – Chryron
    May 8 at 19:43

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