Merge pull request #108 from VilmaPerez/patch-2

Update introduction-to-edna.bib

Author: jfy133

assets/references/introduction-to-edna.bib

@@ -1,33 +1,3 @@
-@article{Unknown2024-lw,
-  title     = {Using {DNA} archived in lake sediments to reconstruct past
-               ecosystems},
-  publisher = {Elsevier},
-  abstract  = {Ecosystems are continuously responding to both natural and
-               anthropogenic environmental change. Lake sediments preserve local
-               and global evidence of th…},
-  month     = jan,
-  year      = 2024,
-  url       = {http://dx.doi.org/10.1016/B978-0-323-99931-1.00171-9},
-  doi       = {10.1016/B978-0-323-99931-1.00171-9}
-}
-
-@article{Unknown2020-ht,
-  title     = {Geochemical identification of potential {DNA}-hotspots and
-               {DNA}-infrared fingerprints in lake sediments},
-  journal   = {Applied Geochemistry},
-  publisher = {Pergamon},
-  volume    = 122,
-  pages     = 104728,
-  abstract  = {DNA preserved in sedimentary materials can be used to study past
-               ecosystem changes, such as species' colonization and extinction.
-               It is believed that …},
-  month     = nov,
-  year      = 2020,
-  url       = {http://dx.doi.org/10.1016/j.apgeochem.2020.104728},
-  doi       = {10.1016/j.apgeochem.2020.104728},
-  issn      = {0883-2927}
-}
-
 @article{Jia2022-vv,
   title     = {Preservation of sedimentary plant {DNA} is related to lake water
                chemistry},
@@ -785,4 +755,191 @@ @article{Jenkins2012-ac
   pmid     = 22798611,
   issn     = {0036-8075,1095-9203}
 }
-
+@article{Pedersen2015,
+  title={Ancient and modern environmental DNA},
+  author={Pedersen, Mikkel Winther and Overballe-Petersen, S{\o}ren and Ermini, Luca and Sarkissian, Clio Der and Haile, James and Hellstrom, Micaela and Spens, Johan and Thomsen, Philip Francis and Bohmann, Kristine and Cappellini, Enrico and others},
+  journal={Philosophical Transactions of the Royal Society B: Biological Sciences},
+  volume={370},
+  number={1660},
+  pages={20130383},
+  year={2015},
+  publisher={The Royal Society}
+}
+@article{Orlando2021,
+  title={Ancient DNA analysis},
+  author={Orlando, Ludovic and Allaby, Robin and Skoglund, Pontus and Der Sarkissian, Clio and Stockhammer, Philipp W and {\'A}vila-Arcos, Mar{\'\i}a C and Fu, Qiaomei and Krause, Johannes and Willerslev, Eske and Stone, Anne C and others},
+  journal={Nature reviews methods primers},
+  volume={1},
+  number={1},
+  pages={14},
+  year={2021},
+  publisher={Nature Publishing Group UK London}
+}
+@incollection{Murchie2023,
+  title={Terrestrial Fauna and Hominin DNA from Sedimentary Archives},
+  author={Murchie, Tyler J and Giguet-Covex, Charline and Heintzman, Peter D and Slon, Viviane and Wang, Yucheng},
+  booktitle={Tracking Environmental Change Using Lake Sediments: Volume 6: Sedimentary DNA},
+  pages={299--378},
+  year={2023},
+  publisher={Springer}
+}
+@article{Capo2021,
+  title={Lake sedimentary DNA research on past terrestrial and aquatic biodiversity: Overview and recommendations},
+  author={Capo, Eric and Giguet-Covex, Charline and Rouillard, Alexandra and Nota, Kevin and Heintzman, Peter D and Vuillemin, Aur{\`e}le and Ariztegui, Daniel and Arnaud, Fabien and Belle, Simon and Bertilsson, Stefan and others},
+  journal={Quaternary},
+  volume={4},
+  number={1},
+  pages={6},
+  year={2021},
+  publisher={MDPI}
+}
+@article{Sand2024,
+  title={Importance of eDNA taphonomy and sediment provenance for robust ecological inference: Insights from interfacial geochemistry},
+  author={Sand, KK and Jelavi{\'c}, S and Kj{\ae}r, KH and Prohaska, A},
+  journal={Environmental DNA},
+  volume={6},
+  number={2},
+  pages={e519},
+  year={2024},
+  publisher={Wiley Online Library}
+}
+@incollection{Garces2023,
+  title={Terrestrial plant DNA from lake sediments},
+  author={Garc{\'e}s-Pastor, Sandra and Nota, Kevin and Rijal, Dilli P and Liu, Sisi and Jia, Weihan and Leunda, Maria and Schw{\"o}rer, Christoph and Crump, Sarah E and Parducci, Laura and Alsos, Inger G},
+  booktitle={Tracking Environmental Change Using Lake Sediments: Volume 6: Sedimentary DNA},
+  pages={275--298},
+  year={2023},
+  publisher={Springer}
+}
+@article{Torti2015,
+  title={Origin, dynamics, and implications of extracellular DNA pools in marine sediments},
+  author={Torti, Andrea and Lever, Mark Alexander and J{\o}rgensen, Bo Barker},
+  journal={Marine genomics},
+  volume={24},
+  pages={185--196},
+  year={2015},
+  publisher={Elsevier}
+}
+@article{Stotzky2000,
+  title={Persistence and biological activity in soil of insecticidal proteins from Bacillus thuringiensis and of bacterial DNA bound on clays and humic acids},
+  author={Stotzky, G},
+  journal={Journal of Environmental Quality},
+  volume={29},
+  number={3},
+  pages={691--705},
+  year={2000},
+  publisher={Wiley Online Library}
+}
+@article{Lorenz1987,
+  title={Adsorption of DNA to sand and variable degradation rates of adsorbed DNA},
+  author={Lorenz, MICHAEL G and Wackernagel, WILFRIED},
+  journal={Applied and environmental microbiology},
+  volume={53},
+  number={12},
+  pages={2948--2952},
+  year={1987},
+  publisher={Am Soc Microbiol}
+}
+@article{Lorenz1981,
+  title={Interaction of marine sediment with DNA and DNA availability to nucleases},
+  author={Lorenz, MG and Aardema, BW and Krumbein, WE},
+  journal={Marine Biology},
+  volume={64},
+  pages={225--230},
+  year={1981},
+  publisher={Springer}
+}
+@article{Beall2009,
+  title={Analysis of oligonucleotide DNA binding and sedimentation properties of montmorillonite clay using ultraviolet light spectroscopy},
+  author={Beall, Gary W and Sowersby, Drew S and Roberts, Rachel D and Robson, Michael H and Lewis, L Kevin},
+  journal={Biomacromolecules},
+  volume={10},
+  number={1},
+  pages={105--112},
+  year={2009},
+  publisher={ACS Publications}
+}
+@article{Armbrecht2020,
+  title={An optimized method for the extraction of ancient eukaryote DNA from marine sediments},
+  author={Armbrecht, Linda and Herrando-P{\'e}rez, Salvador and Eisenhofer, Raphael and Hallegraeff, Gustaaf M and Bolch, Christopher JS and Cooper, Alan},
+  journal={Molecular Ecology Resources},
+  volume={20},
+  number={4},
+  pages={906--919},
+  year={2020},
+  publisher={Wiley Online Library}
+}
+@article{Perez2022,
+  title={A case study for the recovery of authentic microbial ancient DNA from soil samples},
+  author={P{\'e}rez, Vilma and Liu, Yichen and Hengst, Martha B and Weyrich, Laura S},
+  journal={Microorganisms},
+  volume={10},
+  number={8},
+  pages={1623},
+  year={2022},
+  publisher={MDPI}
+}
+@incollection{Heintzman2023,
+  title={The sedimentary ancient DNA workflow},
+  author={Heintzman, Peter D and Nota, Kevin and Rouillard, Alexandra and Lammers, Youri and Murchie, Tyler J and Armbrecht, Linda and Garc{\'e}s-Pastor, Sandra and Vernot, Benjamin},
+  booktitle={Tracking Environmental Change Using Lake Sediments: Volume 6: Sedimentary DNA},
+  pages={53--84},
+  year={2023},
+  publisher={Springer}
+}
+@article{Murchie2021,
+  title={Optimizing extraction and targeted capture of ancient environmental DNA for reconstructing past environments using the PalaeoChip Arctic-1.0 bait-set},
+  author={Murchie, Tyler J and Kuch, Melanie and Duggan, Ana T and Ledger, Marissa L and Roche, Kevin and Klunk, Jennifer and Karpinski, Emil and Hackenberger, Dirk and Sadoway, Tara and MacPhee, Ross and others},
+  journal={Quaternary Research},
+  volume={99},
+  pages={305--328},
+  year={2021},
+  publisher={Cambridge University Press}
+}
+@article{Slon2017,
+  title={Neandertal and Denisovan DNA from Pleistocene sediments},
+  author={Slon, Viviane and Hopfe, Charlotte and Wei{\ss}, Clemens L and Mafessoni, Fabrizio and De La Rasilla, Marco and Lalueza-Fox, Carles and Rosas, Antonio and Soressi, Marie and Knul, Monika V and Miller, Rebecca and others},
+  journal={Science},
+  volume={356},
+  number={6338},
+  pages={605--608},
+  year={2017},
+  publisher={American Association for the Advancement of Science}
+}
+@article{Crump2021,
+  title={Sedimentary ancient DNA as a tool in paleoecology},
+  author={Crump, Sarah E},
+  journal={Nature Reviews Earth \& Environment},
+  volume={2},
+  number={4},
+  pages={229--229},
+  year={2021},
+  publisher={Nature Publishing Group UK London}
+}
+@article{Cribdon2020,
+  title={PIA: more accurate taxonomic assignment of metagenomic data demonstrated on sedaDNA from the North Sea},
+  author={Cribdon, Becky and Ware, Roselyn and Smith, Oliver and Gaffney, Vincent and Allaby, Robin G},
+  journal={Frontiers in Ecology and Evolution},
+  volume={8},
+  pages={84},
+  year={2020},
+  publisher={Frontiers Media SA}
+}
+@incollection{Vuillemin2023,
+  title={Bacterial and archaeal DNA from lake sediments},
+  author={Vuillemin, Aur{\`e}le and Coolen, Marco JL and Kallmeyer, Jens and Liebner, Susanne and Bertilsson, Stefan},
+  booktitle={Tracking Environmental Change Using Lake Sediments: Volume 6: Sedimentary DNA},
+  pages={85--151},
+  year={2023},
+  publisher={Springer}
+}
+@article{Schulte2021,
+  title={Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest},
+  author={Schulte, Luise and Bernhardt, Nadine and Stoof-Leichsenring, Kathleen and Zimmermann, Heike H and Pestryakova, Luidmila A and Epp, Laura S and Herzschuh, Ulrike},
+  journal={Molecular Ecology Resources},
+  volume={21},
+  number={3},
+  pages={801--815},
+  year={2021},
+  publisher={Wiley Online Library}
+}