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Hawaiian_transcriptome.bib
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}
@article{edwards2007database,
title={A database of wing diversity in the {H}awaiian \emph{{D}rosophila}},
author={Edwards, Kevin A and Doescher, Linden T and Kaneshiro, Kenneth Y and Yamamoto, Daisuke},
journal={PLoS One},
volume={2},
number={5},
pages={e487},
year={2007},
publisher={Public Library of Science San Francisco, USA}
}
@article{leader2018flyatlas,
title={FlyAtlas 2: a new version of the \emph{{D}rosophila melanogaster} expression atlas with {R}{N}{A}-Seq, miRNA-Seq and sex-specific data},
author={Leader, David P and Krause, Sue A and Pandit, Aniruddha and Davies, Shireen A and Dow, Julian A T},
journal={Nucleic Acids Research},
volume={46},
number={D1},
pages={D809--D815},
year={2018},
publisher={Oxford University Press}
}
@article{boussau2013genome,
title={Genome-scale coestimation of species and gene trees},
author={Boussau, Bastien and Sz{\"o}ll{\H{o}}si, Gergely J and Duret, Laurent and Gouy, Manolo and Tannier, Eric and Daubin, Vincent},
journal={Genome Research},
volume={23},
number={2},
pages={323--330},
year={2013},
publisher={Cold Spring Harbor Lab}
}
@article{church2021phylotranscriptomics,
title={Phylotranscriptomics reveals discordance in the phylogeny of {H}awaiian \emph{{D}rosophila} and \emph{{S}captomyza} ({D}iptera: {D}rosophilidae)},
author={Church, Samuel H and Extavour, Cassandra G},
journal={bioRxiv},
year={2021},
publisher={Cold Spring Harbor Laboratory}
}
@article{simon2020evolving,
title={An Evolving View of Phylogenetic Support},
author={Simon, Chris},
journal={Systematic Biology},
year={2020},
pages={syaa068}
}
#Branch supports—sometimes called nodal supports—measure how much of the information in the data set used to create a particular tree supports each internal branch in that tree.
@incollection{swofford1996phylogenetic,
author={Swofford, DL, and Olsen GJ, and Waddell PJ},
title={Phylogenetic inference},
editor={Hillis, DM, and Moritz, C, and Mable, BK},
booktitle={Molecular Systematics},
publisher={Sinauer},
address={Sunderland, MA},
year={1996},
chapter={11},
pages={407--514},
}
#Intuitively, the challenge of mapping reads to fragmented gene models should diminish the robustness of expression estimates
@article{freedman2021error,
title={Error, noise and bias in de novo transcriptome assemblies},
author={Freedman, Adam H and Clamp, Michele and Sackton, Timothy B},
journal={Molecular Ecology Resources},
volume={21},
number={1},
pages={18--29},
year={2021},
publisher={Wiley Online Library}
}
@article{breschi2016gene,
title={Gene-specific patterns of expression variation across organs and species},
author={Breschi, Alessandra and Djebali, Sarah and Gillis, Jesse and Pervouchine, Dmitri D and Dobin, Alex and Davis, Carrie A and Gingeras, Thomas R and Guig{\'o}, Roderic},
journal={Genome Biology},
volume={17},
number={1},
pages={1--13},
year={2016},
publisher={Springer}
}
@article{tung2014linear,
title={A linear-time algorithm for Gaussian and non-Gaussian trait evolution models},
author={Tung Ho, Lam si and An{\'e}, C{\'e}cile},
journal={Systematic Biology},
volume={63},
number={3},
pages={397--408},
year={2014},
publisher={Oxford University Press}
}
@article{church2021phylotranscriptomics,
title={Phylotranscriptomics reveals discordance in the phylogeny of {H}awaiian \emph{{D}rosophila} and \emph{{S}captomyza} ({D}iptera: {D}rosophilidae)},
author={Church, Samuel H and Extavour, Cassandra G},
journal={bioRxiv},
year={2021},
publisher={Cold Spring Harbor Laboratory}
}
@article{obbard2012estimating,
title={Estimating divergence dates and substitution rates in the \emph{{D}rosophila} phylogeny},
author={Obbard, Darren J and Maclennan, John and Kim, Kang-Wook and Rambaut, Andrew and O’Grady, Patrick M and Jiggins, Francis M},
journal={Molecular Biology and Evolution},
volume={29},
number={11},
pages={3459--3473},
year={2012},
publisher={Oxford University Press}
}
@article{chen2019quantitative,
title={A quantitative framework for characterizing the evolutionary history of mammalian gene expression},
author={Chen, Jenny and Swofford, Ross and Johnson, Jeremy and Cummings, Beryl B and Rogel, Noga and Lindblad-Toh, Kerstin and Haerty, Wilfried and Di Palma, Federica and Regev, Aviv},
journal={Genome Research},
volume={29},
number={1},
pages={53--63},
year={2019},
publisher={Cold Spring Harbor Lab}
}
@article{rohlfs2014modeling,
title={Modeling gene expression evolution with an extended Ornstein--Uhlenbeck process accounting for within-species variation},
author={Rohlfs, Rori V and Harrigan, Patrick and Nielsen, Rasmus},
journal={Molecular Biology and evolution},
volume={31},
number={1},
pages={201--211},
year={2014},
publisher={Oxford University Press}
}
@article{el2021gene,
title={Gene expression dynamics during rapid organismal diversification in African cichlid fishes},
author={El Taher, Athimed and B{\"o}hne, Astrid and Boileau, Nicolas and Ronco, Fabrizia and Indermaur, Adrian and Widmer, Lukas and Salzburger, Walter},
journal={Nature Ecology \& evolution},
volume={5},
number={2},
pages={243--250},
year={2021},
publisher={Nature Publishing Group}
}
@article{kalinka2010gene,
title={Gene expression divergence recapitulates the developmental hourglass model},
author={Kalinka, Alex T and Varga, Karolina M and Gerrard, Dave T and Preibisch, Stephan and Corcoran, David L and Jarrells, Julia and Ohler, Uwe and Bergman, Casey M and Tomancak, Pavel},
journal={Nature},
volume={468},
number={7325},
pages={811--814},
year={2010},
publisher={Nature Publishing Group}
}
@article{bedford2009optimization,
title={Optimization of gene expression by natural selection},
author={Bedford, Trevor and Hartl, Daniel L},
journal={Proceedings of the National Academy of Sciences},
volume={106},
number={4},
pages={1133--1138},
year={2009},
publisher={National Acad Sciences}
}
@article{cardoso2019gene,
title={Gene expression across mammalian organ development},
author={Cardoso-Moreira, Margarida and Halbert, Jean and Valloton, Delphine and Velten, Britta and Chen, Chunyan and Shao, Yi and Liechti, Ang{\'e}lica and Ascen{\c{c}}{\~a}o, Kelly and Rummel, Coralie and Ovchinnikova, Svetlana and others},
journal={Nature},
volume={571},
number={7766},
pages={505--509},
year={2019},
publisher={Nature Publishing Group}
}
@article{fukushima2020amalgamated,
title={Amalgamated cross-species transcriptomes reveal organ-specific propensity in gene expression evolution},
author={Fukushima, Kenji and Pollock, David D},
journal={Nature Communications},
volume={11},
number={1},
pages={1--14},
year={2020},
publisher={Nature Publishing Group}
}
@article{gilad2015reanalysis,
title={A reanalysis of mouse {E}{N}{C}{O}{D}{E} comparative gene expression data},
author={Gilad, Yoav and Mizrahi-Man, Orna},
journal={F1000Research},
volume={4},
year={2015},
pages={1--30},
publisher={Faculty of 1000 Ltd}
}
@article{dunn2013phylogenetic,
title={Phylogenetic analysis of gene expression},
author={Dunn, Casey W and Luo, Xi and Wu, Zhijin},
journal={Integrative and Comparative Biology},
volume={53},
number={5},
pages={847--856},
year={2013},
publisher={Oxford University Press}
}
@article{lin2014comparison,
title={Comparison of the transcriptional landscapes between human and mouse tissues},
author={Lin, Shin and Lin, Yiing and Nery, Joseph R and Urich, Mark A and Breschi, Alessandra and Davis, Carrie A and Dobin, Alexander and Zaleski, Christopher and Beer, Michael A and Chapman, William C and others},
journal={Proceedings of the National Academy of Sciences},
volume={111},
number={48},
pages={17224--17229},
year={2014},
publisher={National Acad Sciences}
}
@article{yanai2004incongruent,
title={Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control},
author={Yanai, Itai and Graur, Dan and Ophir, Ron},
journal={Omics: a Journal of Integrative Biology},
volume={8},
number={1},
pages={15--24},
year={2004},
publisher={Mary Ann Liebert, Inc.}
}
@article{liao2006evolutionary,
title={Evolutionary conservation of expression profiles between human and mouse orthologous genes},
author={Liao, Ben-Yang and Zhang, Jianzhi},
journal={Molecular Biology and Evolution},
volume={23},
number={3},
pages={530--540},
year={2006},
publisher={Oxford University Press}
}
@article{merkin2012evolutionary,
title={Evolutionary dynamics of gene and isoform regulation in Mammalian tissues},
author={Merkin, Jason and Russell, Caitlin and Chen, Ping and Burge, Christopher B},
journal={Science},
volume={338},
number={6114},
pages={1593--1599},
year={2012},
publisher={American Association for the Advancement of Science}
}
@article{barbosa2012evolutionary,
title={The evolutionary landscape of alternative splicing in vertebrate species},
author={Barbosa-Morais, Nuno L and Irimia, Manuel and Pan, Qun and Xiong, Hui Y and Gueroussov, Serge and Lee, Leo J and Slobodeniuc, Valentina and Kutter, Claudia and Watt, Stephen and {\c{C}}olak, Recep and others},
journal={Science},
volume={338},
number={6114},
pages={1587--1593},
year={2012},
publisher={American Association for the Advancement of Science}
}
@article{brawand2011evolution,
title={The evolution of gene expression levels in mammalian organs},
author={Brawand, David and Soumillon, Magali and Necsulea, Anamaria and Julien, Philippe and Cs{\'a}rdi, G{\'a}bor and Harrigan, Patrick and Weier, Manuela and Liechti, Ang{\'e}lica and Aximu-Petri, Ayinuer and Kircher, Martin and others},
journal={Nature},
volume={478},
number={7369},
pages={343--348},
year={2011},
publisher={Nature Publishing Group}
}
@article{li2011rsem,
title={RSEM: accurate transcript quantification from {R}{N}{A}-Seq data with or without a reference genome},
author={Li, Bo and Dewey, Colin N},
journal={BMC Bioinformatics},
volume={12},
number={1},
pages={1--16},
year={2011},
publisher={Springer}
}
#General reference and good citation for phylogenetic methods
@article{larkin2021flybase,
title={FlyBase: updates to the \emph{{D}rosophila} melanogaster knowledge base},
author={Larkin, Aoife and Marygold, Steven J and Antonazzo, Giulia and Attrill, Helen and Dos Santos, Gilberto and Garapati, Phani V and Goodman, Joshua L and Gramates, L Sian and Millburn, Gillian and Strelets, Victor B and others},
journal={Nucleic Acids Research},
volume={49},
number={D1},
pages={D899--D907},
year={2021},
publisher={Oxford University Press}
}
@article{pease2016phylogenomics,
title={Phylogenomics reveals three sources of adaptive variation during a rapid radiation},
author={Pease, James B and Haak, David C and Hahn, Matthew W and Moyle, Leonie C},
journal={PLoS Biology},
volume={14},
number={2},
pages={e1002379},
year={2016},
publisher={Public Library of Science San Francisco, CA USA}
}
# Recent studies have begun to uncover several intriguing patterns of phylogenomic
divergence, especially in rapidly radiating groups. One such pattern is a persistent discordance among genes for particular phylogenetic relationships, regardless of the quantity or quality of molecular data sampled.
@article{baker1997multiple,
title={Multiple sources of character information and the phylogeny of {H}awaiian drosophilids},
author={Baker, Richard H and DeSalle, Rob},
journal={Systematic Biology},
volume={46},
number={4},
pages={654--673},
year={1997},
publisher={Society of Systematic Biologists}
}
@article{kim2020highly,
title={Highly contiguous assemblies of 101 drosophilid genomes},
author={Kim, Bernard Y and Wang, Jeremy R and Miller, Danny E and Barmina, Olga and Delaney, Emily and Thompson, Ammon and Comeault, Aaron A and Peede, David and D’Agostino, Emmanuel RR and Pelaez, Julianne and others},
journal={bioRxiv},
year={2020},
volume={422775},
publisher={Cold Spring Harbor Laboratory}
}
@article{lapoint2011phylogenetic,
title={Phylogenetic relationships in the spoon tarsus subgroup of {H}awaiian \emph{{D}rosophila}: conflict and concordance between gene trees},
author={Lapoint, Richard T and Gidaya, Alexander and O’Grady, Patrick M},
journal={Molecular Phylogenetics and Evolution},
volume={58},
number={3},
pages={492--501},
year={2011},
publisher={Elsevier}
}
@article{bonacum2005phylogeny,
title={Phylogeny and age of diversification of the planitibia species group of the {H}awaiian \emph{{D}rosophila}},
author={Bonacum, James and O’Grady, Patrick M and Kambysellis, Michael and DeSalle, Rob},
journal={Molecular Phylogenetics and Evolution},
volume={37},
number={1},
pages={73--82},
year={2005},
publisher={Elsevier}
}
@article{o2004phylogenetic,
title={Phylogenetic relationships within the \emph{{D}rosophila} haleakalae species group inferred by molecular and morphological characters ({D}iptera: {D}rosophilidae)},
author={O’Grady, PATRICK M and Zilversmit, Martine},
journal={Bishop Museum Bulletin in Entomology},
volume={12},
pages={117--134},
year={2004}
}
@article{kambysellis1971studies,
title={Studies of oogenesis in natural populations of {D}rosophilidae. I. Relation of ovarian development and ecological habitats of the {H}awaiian species},
author={Kambysellis, MP and Heed, WB},
journal={The American Naturalist},
volume={105},
number={941},
pages={31--49},
year={1971},
publisher={University of Chicago Press}
}
@article{bryan1938key,
title={Key to the {H}awaiian {D}rosophilidae and Descriptions of New Species},
author={Bryan JR, Edwin H},
journal={Proceedings of the Hawaiian Entomological Society},
volume={10},
number={1},
year={1938},
pages={25--42}
}
@article{kodandaramaiah2011tectonic,
title={Tectonic calibrations in molecular dating},
author={Kodandaramaiah, Ullasa},
journal={Current Zoology},
volume={57},
number={1},
pages={116--124},
year={2011},
publisher={Oxford University Press Oxford, UK}
}
@article{castresana2000selection,
title={Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis},
author={Castresana, Jose},
journal={Molecular Biology and Evolution},
volume={17},
number={4},
pages={540--552},
year={2000},
publisher={Oxford University Press}
}
@article{montague1981reproductive,
title={Reproductive allocation in the {H}awaiian {D}rosophilidae: egg size and number},
author={Montague, Jeremy R and Mangan, Robert L and Starmer, William T},
journal={The American Naturalist},
volume={118},
number={6},
pages={865--871},
year={1981},
publisher={University of Chicago Press}
}
@article{edwards2007database,
title={A database of wing diversity in the {H}awaiian \emph{{D}rosophila}},
author={Edwards, Kevin A and Doescher, Linden T and Kaneshiro, Kenneth Y and Yamamoto, Daisuke},
journal={PLoS One},
volume={2},
number={5},
pages={e487},
year={2007},
publisher={Public Library of Science}
}
@article{sarikaya2019reproductive,
title={Reproductive capacity evolves in response to ecology through common changes in cell number in {H}awaiian \emph{{D}rosophila}},
author={Sarikaya, Didem P and Church, Samuel H and Lagomarsino, Laura P and Magnacca, Karl N and Montgomery, Steven L and Price, Donald K and Kaneshiro, Kenneth Y and Extavour, Cassandra G},
journal={Current Biology},
volume={29},
number={11},
pages={1877--1884},
year={2019},
publisher={Elsevier}
}
@article{carson1969polytene,
title={Polytene chromosome relationships in {H}awaiian species of \emph{{D}rosophila}. IV. The D. primaeva subgroup},
author={Carson, HL and Stalker, HD},
journal={Univ. Tex. Publ},
volume={6918},
pages={85--94},
year={1969}
}
@article{lapoint2013diversification,
title={Diversification and dispersal of the {H}awaiian {D}rosophilidae: the evolution of \emph{{S}captomyza}},
author={Lapoint, Richard T and O’Grady, Patrick M and Whiteman, Noah K},
journal={Molecular Phylogenetics and Evolution},
volume={69},
number={1},
pages={95--108},
year={2013},
publisher={Elsevier}
}
@book{hardy1965insects,
title={{D}iptera: {C}yclorrhapha {II}, {S}eries {S}chizophora {S}ection {A}calypterae {I}. Family {D}rosophilidae.},
author={Hardy, D},
volume={12},
booktitle={Insects of {H}awaii},
year={1965},
publisher={University of Hawai'i Press}
}
@article{katoh2017multiple,
title={Multiple origins of {H}awaiian drosophilids: phylogeography of \emph{{S}captomyza} hardy ({D}iptera: {D}rosophilidae)},
author={Katoh, Toru and Izumitani, Hiroyuki F and Yamashita, Shinji and Watada, Masayoshi},
journal={Entomological Science},
volume={20},
number={1},
pages={33--44},
year={2017},
publisher={Wiley Online Library}
}
@article{throckmorton1966relationships,
title={The relationships of the endemic {H}awaiian {D}rosophilidae},
author={Throckmorton, Lynn H},
journal={University of Texas Publications},
volume={6615},
pages={335--396},
year={1966}
}
@article{heed1968ecology,
title={Ecology of the {H}awaiian {D}rosophilidae},
author={Heed, W B},
journal={University of Texas Publications},
volume={6818},
pages={387-–418},
year={1968}
}
#figure suggests two introductions to Hawaii
@article{kambysellis1995pattern,
title={Pattern of ecological shifts in the diversification of {H}awaiian \emph{{D}rosophila} inferred from a molecular phylogeny},
author={Kambysellis, Michael P and Ho, Kin-Fan and Craddock, Elysse M and Piano, Fabio and Parisi, Michael and Cohen, Jacob},
journal={Current Biology},
volume={5},
number={10},
pages={1129--1139},
year={1995},
publisher={Elsevier}
}
@article{kambysellis1971studies,
title={Studies of oogenesis in natural populations of {D}rosophilidae. I. Relation of ovarian development and ecological habitats of the {H}awaiian species},
author={Kambysellis, MP and Heed, WB},
journal={The American Naturalist},
volume={105},
number={941},
pages={31--49},
year={1971},
publisher={University of Chicago Press}
}
@article{stevenson1995organ,
title={Organ and cell allometry in {H}awaiian \emph{{D}rosophila}: how to make a big fly},
author={Stevenson, RD and Hill, Mark F and Bryant, Peter J},
journal={Proceedings of the Royal Society of London. Series B: Biological Sciences},
volume={259},
number={1355},
pages={105--110},
year={1995},
publisher={The Royal Society London}
}
@article{magnacca2008review,
title={A review of the endemic {H}awaiian {D}rosophilidae and their host plants},
author={Magnacca, Karl N and Foote, David and O’Grady, Patrick M},
journal={Zootaxa},
volume={1728},
number={1},
pages={1--58},
year={2008}
}
@article{beverley1985ancient,
title={Ancient origin for {H}awaiian {D}rosophilinae inferred from protein comparisons},
author={Beverley, Stephen M and Wilson, Allan C},
journal={Proceedings of the National Academy of Sciences},
volume={82},
number={14},
pages={4753--4757},
year={1985},
publisher={National Acad Sciences}
}
@article{thomas1991molecular,
title={The molecular evolution of the alcohol dehydrogenase locus and the phylogeny of {H}awaiian \emph{{D}rosophila}.},
author={Thomas, Richard H and Hunt, John A},
journal={Molecular Biology and Evolution},
volume={8},
number={5},
pages={687--702},
year={1991}
}
@article{hoang2018ufboot2,
title={UFBoot2: improving the ultrafast bootstrap approximation},
author={Hoang, Diep Thi and Chernomor, Olga and Von Haeseler, Arndt and Minh, Bui Quang and Vinh, Le Sy},
journal={Molecular Biology and Evolution},
volume={35},
number={2},
pages={518--522},
year={2018},
publisher={Oxford University Press}
}
@article{chernomor2016terrace,
title={Terrace aware data structure for phylogenomic inference from supermatrices},
author={Chernomor, Olga and Von Haeseler, Arndt and Minh, Bui Quang},
journal={Systematic Biology},
volume={65},
number={6},
pages={997--1008},
year={2016},
publisher={Oxford University Press}
}
@article{revell2012phytools,
title={phytools: an R package for phylogenetic comparative biology (and other things)},
author={Revell, Liam J},
journal={Methods in Ecology and Evolution},
volume={3},
number={2},
pages={217--223},
year={2012},
publisher={Wiley Online Library}
}
@article{huelsenbeck2003stochastic,
title={Stochastic mapping of morphological characters},
author={Huelsenbeck, John P and Nielsen, Rasmus and Bollback, Jonathan P},
journal={Systematic Biology},
volume={52},
number={2},
pages={131--158},
year={2003},
publisher={Society of Systematic Zoology}
}
@article{kalyaanamoorthy2017modelfinder,
title={ModelFinder: fast model selection for accurate phylogenetic estimates},
author={Kalyaanamoorthy, Subha and Minh, Bui Quang and Wong, Thomas KF and Von Haeseler, Arndt and Jermiin, Lars S},
journal={Nature Methods},
volume={14},
number={6},
pages={587--589},
year={2017},
publisher={Nature Publishing Group}
}
@inproceedings{helfrich2018treeannotator,
title={TreeAnnotator: versatile visual annotation of hierarchical text relations},
author={Helfrich, Philipp and Rieb, Elias and Abrami, Giuseppe and L{\"u}cking, Andy and Mehler, Alexander},
booktitle={Proceedings of the Eleventh International Conference on Language Resources and Evaluation ({LREC} 2018)},
year={2018}
}
@article{rambaut2018posterior,
title={Posterior summarization in {B}ayesian phylogenetics using Tracer 1.7},
author={Rambaut, Andrew and Drummond, Alexei J and Xie, Dong and Baele, Guy and Suchard, Marc A},