1 line
43 KiB
Plaintext
1 line
43 KiB
Plaintext
{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,12,12]],"date-time":"2023-12-12T17:04:10Z","timestamp":1702400650256},"reference-count":144,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,3,7]],"date-time":"2023-03-07T00:00:00Z","timestamp":1678147200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Plant Sci."],"abstract":"<jats:p>Sapindales is an angiosperm order of high economic and ecological value comprising nine families, c. 479 genera, and c. 6570 species. However, family and subfamily relationships in Sapindales remain unclear, making reconstruction of the order\u2019s spatio-temporal and morphological evolution difficult. In this study, we used Angiosperms353 target capture data to generate the most densely sampled phylogenetic trees of Sapindales to date, with 448 samples and c. 85% of genera represented. The percentage of paralogous loci and allele divergence was characterized across the phylogeny, which was time-calibrated using 29 rigorously assessed fossil calibrations. All families were supported as monophyletic. Two core family clades subdivide the order, the first comprising Kirkiaceae, Burseraceae, and Anacardiaceae, the second comprising Simaroubaceae, Meliaceae, and Rutaceae. Kirkiaceae is sister to Burseraceae and Anacardiaceae, and, contrary to current understanding, Simaroubaceae is sister to Meliaceae and Rutaceae. Sapindaceae is placed with Nitrariaceae and Biebersteiniaceae as sister to the core Sapindales families, but the relationships between these families remain unclear, likely due to their rapid and ancient diversification. Sapindales families emerged in rapid succession, coincident with the climatic change of the Mid-Cretaceous Hothouse event. Subfamily and tribal relationships within the major families need revision, particularly in Sapindaceae, Rutaceae and Meliaceae. Much of the difficulty in reconstructing relationships at this level may be caused by the prevalence of paralogous loci, particularly in Meliaceae and Rutaceae, that are likely indicative of ancient gene duplication events such as hybridization and polyploidization playing a role in the evolutionary history of these families. This study provides key insights into factors that may affect phylogenetic reconstructions in Sapindales across multiple scales, and provides a state-of-the-art phylogenetic framework for further research.<\/jats:p>","DOI":"10.3389\/fpls.2023.1063174","type":"journal-article","created":{"date-parts":[[2023,3,7]],"date-time":"2023-03-07T05:48:45Z","timestamp":1678168125000},"update-policy":"http:\/\/dx.doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":5,"title":["Phylogenomic analyses of Sapindales support new family relationships, rapid Mid-Cretaceous Hothouse diversification, and heterogeneous histories of gene duplication"],"prefix":"10.3389","volume":"14","author":[{"given":"Elizabeth M.","family":"Joyce","sequence":"first","affiliation":[]},{"given":"Marc S.","family":"Appelhans","sequence":"additional","affiliation":[]},{"given":"Sven","family":"Buerki","sequence":"additional","affiliation":[]},{"given":"Martin","family":"Cheek","sequence":"additional","affiliation":[]},{"given":"Jurriaan M.","family":"de Vos","sequence":"additional","affiliation":[]},{"given":"Jos\u00e9 R.","family":"Pirani","sequence":"additional","affiliation":[]},{"given":"Alexandre R.","family":"Zuntini","sequence":"additional","affiliation":[]},{"given":"Julien B.","family":"Bachelier","sequence":"additional","affiliation":[]},{"given":"Michael J.","family":"Bayly","sequence":"additional","affiliation":[]},{"given":"Martin W.","family":"Callmander","sequence":"additional","affiliation":[]},{"given":"Marcelo F.","family":"Devecchi","sequence":"additional","affiliation":[]},{"given":"Susan K.","family":"Pell","sequence":"additional","affiliation":[]},{"given":"Milton","family":"Groppo","sequence":"additional","affiliation":[]},{"suffix":"II","given":"Porter P.","family":"Lowry","sequence":"additional","affiliation":[]},{"given":"John","family":"Mitchell","sequence":"additional","affiliation":[]},{"given":"Carolina M.","family":"Siniscalchi","sequence":"additional","affiliation":[]},{"given":"J\u00e9r\u00f4me","family":"Munzinger","sequence":"additional","affiliation":[]},{"given":"Harvey K.","family":"Orel","sequence":"additional","affiliation":[]},{"given":"Caroline M.","family":"Pannell","sequence":"additional","affiliation":[]},{"given":"Lars","family":"Nauheimer","sequence":"additional","affiliation":[]},{"given":"Herv\u00e9","family":"Sauquet","sequence":"additional","affiliation":[]},{"given":"Andrea","family":"Weeks","sequence":"additional","affiliation":[]},{"given":"Alexandra N.","family":"Muellner-Riehl","sequence":"additional","affiliation":[]},{"given":"Ilia J.","family":"Leitch","sequence":"additional","affiliation":[]},{"given":"Olivier","family":"Maurin","sequence":"additional","affiliation":[]},{"given":"F\u00e9lix","family":"Forest","sequence":"additional","affiliation":[]},{"given":"Katharina","family":"Nargar","sequence":"additional","affiliation":[]},{"given":"Kevin R.","family":"Thiele","sequence":"additional","affiliation":[]},{"given":"William J.","family":"Baker","sequence":"additional","affiliation":[]},{"given":"Darren M.","family":"Crayn","sequence":"additional","affiliation":[]}],"member":"1965","published-online":{"date-parts":[[2023,3,7]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1007\/s40415-021-00768-y","article-title":"What reproductive traits tell us about the evolution and diversification of the tree-of-heaven family, simaroubaceae","volume":"45","author":"Alves","year":"2022","journal-title":"Braz. J. Bot."},{"key":"B2","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1111\/boj.12385","article-title":"An update of the angiosperm phylogeny group classification for the orders and families of flowering plants: APG IV","volume":"181","year":"2016","journal-title":"Bot. J. Linn. Soc"},{"key":"B3","doi-asserted-by":"publisher","first-page":"1035","DOI":"10.1002\/tax.12543","article-title":"A new subfamily classification of the citrus family (Rutaceae) based on six nuclear and plastid markers","volume":"70","author":"Appelhans","year":"2021","journal-title":"Taxon"},{"key":"B4","doi-asserted-by":"publisher","first-page":"1235","DOI":"10.1111\/j.1365-2699.2012.02686.x","article-title":"Age and historical biogeography of the pantropically distributed spathelioideae (Rutaceae, sapindales)","volume":"39","author":"Appelhans","year":"2012","journal-title":"J. Biogeogr."},{"key":"B5","doi-asserted-by":"publisher","first-page":"1259","DOI":"10.1093\/aob\/mcr076","article-title":"Phylogeny, evolutionary trends and classification of the Spathelia\u2013Ptaeroxylon clade: Morphological and molecular insights","volume":"107","author":"Appelhans","year":"2011","journal-title":"Ann. Bot."},{"key":"B6","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1002\/ajb2.1416","article-title":"Fossil evidence for a Cretaceous rise of the mahogany family","volume":"107","author":"Atkinson","year":"2020","journal-title":"Am. J. Bot."},{"key":"B7","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1093\/aob\/mcn139","article-title":"Floral structure of Kirkia (Kirkiaceae) and its position in sapindales","volume":"102","author":"Bachelier","year":"2008","journal-title":"Ann. Bot."},{"key":"B8","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1017\/CBO9781139013321.008","article-title":"Comparative floral structure and development of nitrariaceae (Sapindales) and systematic implications","volume-title":"Flowers on the tree of life","author":"Bachelier","year":"2011"},{"key":"B9","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1093\/sysbio\/syab035","article-title":"A comprehensive phylogenomic platform for exploring the angiosperm tree of life","volume":"71","author":"Baker","year":"2022","journal-title":"Syst. Biol."},{"key":"B10","doi-asserted-by":"publisher","first-page":"1059","DOI":"10.1002\/ajb2.1703","article-title":"Exploring Angiosperms353: An open, community toolkit for collaborative phylogenomic research on flowering plants","volume":"108","author":"Baker","year":"2021","journal-title":"Am. J. Bot."},{"key":"B11","doi-asserted-by":"publisher","first-page":"8310","DOI":"10.1038\/s41598-017-08234-0","article-title":"CO2 and temperature decoupling at the million-year scale during the Cretaceous greenhouse","volume":"7","author":"Barral","year":"2017","journal-title":"Sci. Rep."},{"key":"B12","doi-asserted-by":"publisher","first-page":"234","DOI":"10.1111\/boj.12399","article-title":"An introduction to plant phylogenomics with a focus on palms","volume":"182","author":"Barrett","year":"2016","journal-title":"Bot. J. Linn. Soc"},{"key":"B13","volume-title":"Genera plantarum","author":"Bentham","year":"1862"},{"key":"B14","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A flexible trimmer for illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.1660","article-title":"AMAS: A fast tool for alignment manipulation and computing of summary statistics","volume":"4","author":"Borowiec","year":"2016","journal-title":"PeerJ"},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1006650","article-title":"BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis","volume":"15","author":"Bouckaert","year":"2019","journal-title":"PloS Comput. Biol."},{"key":"B17","doi-asserted-by":"publisher","first-page":"1059","DOI":"10.1111\/1755-0998.12449","article-title":"Exon capture phylogenomics: efficacy across scales of divergence","volume":"16","author":"Bragg","year":"2016","journal-title":"Mol. Ecol. Resour."},{"key":"B18","doi-asserted-by":"publisher","first-page":"1234","DOI":"10.1002\/ajb2.1693","article-title":"An updated infra-familial classification of sapindaceae based on targeted enrichment data","volume":"108","author":"Buerki","year":"2021","journal-title":"Am. J. Bot."},{"key":"B19","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1093\/aob\/mct106","article-title":"The abrupt climate change at the Eocene\u2013oligocene boundary and the emergence of south-East Asia triggered the spread of sapindaceous lineages","volume":"112","author":"Buerki","year":"2013","journal-title":"Ann. Bot."},{"key":"B20","doi-asserted-by":"publisher","first-page":"148","DOI":"10.5091\/plecevo.2010.437","article-title":"Phylogeny and circumscription of sapindaceae revisited: Molecular sequence data, morphology and biogeography support recognition of a new family, xanthoceraceae","volume":"143","author":"Buerki","year":"2010","journal-title":"Plant Ecol. Evol."},{"key":"B21","doi-asserted-by":"publisher","first-page":"1767","DOI":"10.3732\/ajb.91.11.1767","article-title":"Miocene Winged fruits of loxopterygium (Anacardiaceae) from the Ecuadorian Andes","volume":"91","author":"Burnham","year":"2004","journal-title":"Am. J. Bot."},{"key":"B22","doi-asserted-by":"publisher","first-page":"1821","DOI":"10.3732\/ajb.94.11.1821","article-title":"Swietenia (Meliaceae) flower in late oligocene\u2013early Miocene amber from simojovel de allende, chiapas, Mexico","volume":"94","author":"Casta\u00f1eda-Posadas","year":"2007","journal-title":"Am. J. Bot."},{"key":"B23","doi-asserted-by":"crossref","volume-title":"The lower tertiary floras of southern England: I Palaeocene floras, London clay flora (Supplement)","author":"Chandler","year":"1961","DOI":"10.5962\/bhl.title.110079"},{"key":"B24","doi-asserted-by":"publisher","first-page":"1191","DOI":"10.2307\/2656983","article-title":"Phylogenetic relationships of rutaceae: A cladistic analysis of the subfamilies using evidence from rbcL and atpB sequence variation","volume":"86","author":"Chase","year":"1999","journal-title":"Am. J. Bot."},{"key":"B25","doi-asserted-by":"publisher","first-page":"528","DOI":"10.2307\/2399846","article-title":"Phylogenetics of seed plants: An analysis of nucleotide sequences from the plastid gene rbcL","volume":"80","author":"Chase","year":"1993","journal-title":"Ann. Mo. Bot. Gard."},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2022.958138","article-title":"Identification of early quassinoid biosynthesis in the invasive tree of heaven (Ailanthus altissima) confirms evolutionary origin from protolimonoids","volume":"13","author":"Chuang","year":"2022","journal-title":"Front. Plant Sci."},{"key":"B27","first-page":"408","article-title":"Simaroubaceae","volume-title":"The families and genera of vascular plants - eudicots: Sapindales, cucurbitales, myrtaceae","author":"Clayton","year":"2011"},{"key":"B28","doi-asserted-by":"publisher","first-page":"1325","DOI":"10.1086\/521796","article-title":"Molecular phylogeny of the tree-of-heaven family (Simaroubaceae) based on chloroplast and nuclear markers","volume":"168","author":"Clayton","year":"2007","journal-title":"Int. J. Plant Sci."},{"key":"B29","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1093\/sysbio\/syp041","article-title":"Recent long-distance dispersal overshadows ancient biogeographical patterns in a pantropical angiosperm family (Simaroubaceae, sapindales)","volume":"58","author":"Clayton","year":"2009","journal-title":"Syst. Biol."},{"key":"B30","volume-title":"Fossil fruits and seeds of the middle Eocene messel biota, Germany","author":"Collinson","year":"2012"},{"key":"B31","doi-asserted-by":"publisher","first-page":"1","DOI":"10.5962\/bhl.title.100826","article-title":"A preliminary survey of fossil leaves and well-preserved reproductive structures from the sentinel butte formation (Paleocene) near almont, north Dakota","volume":"20","author":"Crane","year":"1990","journal-title":"Fieldiana Geol. New Ser."},{"key":"B32","doi-asserted-by":"publisher","first-page":"291","DOI":"10.3732\/ajb.1100356","article-title":"Targeted enrichment strategies for next-generation plant biology","volume":"99","author":"Cronn","year":"2012","journal-title":"Am. J. Bot."},{"key":"B33","volume-title":"The evolution and classification of flowering plants","author":"Cronquist","year":"1968"},{"key":"B34","first-page":"76","article-title":"Burseraceae","volume-title":"The families and genera of vascular plants - eudicots: Sapindales, cucurbitales, myrtaceae","author":"Daly","year":"2011"},{"key":"B35","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1111\/nph.13367","article-title":"Confluence, synnovation, and depauperons in plant diversification","volume":"207","author":"Donoghue","year":"2015","journal-title":"New Phytol."},{"key":"B36","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1111\/j.1759-6831.2012.00236.x","article-title":"The unbearable uncertainty of Bayesian divergence time estimation","volume":"51","author":"Dos Reis","year":"2013","journal-title":"J. Syst. Evol."},{"key":"B37","first-page":"11","article-title":"Genomic plant DNA preparation from fresh tissue-CTAB method","volume":"19","author":"Doyle","year":"1987","journal-title":"Phytochem. Bull."},{"key":"B38","first-page":"367","article-title":"Anacardiaceae","volume-title":"Flora brasiliensis","author":"Engler","year":"1876"},{"key":"B39","first-page":"187","article-title":"Rutaceae","volume-title":"Die nat\u00fcrlichen pflanzenfamilien","author":"Engler","year":"1931"},{"key":"B40","doi-asserted-by":"publisher","first-page":"1179","DOI":"10.3732\/ajb.0900234","article-title":"Upper Cretaceous woods from the olmos formation (late campanian\u2013early maastrichtian), coahuila, Mexico","volume":"97","author":"Estrada-Ruiz","year":"2010","journal-title":"Am. J. Bot."},{"key":"B41","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1007\/s40415-021-00733-9","article-title":"Nortriterpenes, chromones, anthraquinones, and their chemosystematics significance in meliaceae, rutaceae, and simaroubaceae (Sapindales)","volume":"45","author":"Fernandes da Silva","year":"2022","journal-title":"Braz. J. Bot."},{"key":"B42","doi-asserted-by":"publisher","first-page":"99","DOI":"10.2307\/2412448","article-title":"Distinguishing homologous from analogous proteins","volume":"19","author":"Fitch","year":"1970","journal-title":"Syst. Biol."},{"key":"B43","doi-asserted-by":"publisher","first-page":"338","DOI":"10.1093\/sysbio\/syw086","article-title":"Evaluating the impact of genomic data and priors on Bayesian estimates of the angiosperm evolutionary timescale","volume":"66","author":"Foster","year":"2017","journal-title":"Syst. Biol."},{"key":"B44","doi-asserted-by":"publisher","first-page":"416","DOI":"10.1038\/s41597-020-00702-z","article-title":"LCVP, the Leipzig catalogue of vascular plants, a new taxonomic reference list for all known vascular plants","volume":"416","author":"Freiberg","year":"2020","journal-title":"Sci. Data"},{"key":"B45","doi-asserted-by":"publisher","first-page":"802","DOI":"10.1002\/j.1537-2197.1996.tb12769.x","article-title":"Sapindales: Molecular delimitation and infraordinal groups","volume":"83","author":"Gadek","year":"1996","journal-title":"Am. J. Bot."},{"key":"B46","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1007\/s40415-021-00719-7","article-title":"Pollen morphology and evolutionary history of sapindales","volume":"45","author":"Gon\u00e7alves-Esteves","year":"2022","journal-title":"Braz. J. Bot."},{"key":"B47","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1080\/00173134.2019.1696400","article-title":"Combined LM and SEM study of the middle Miocene (Sarmatian) palynoflora from the lavanttal basin, Austria: Part v. magnoliophyta 3 \u2013 myrtales to ericales","volume":"59","author":"Gr\u00edmsson","year":"2020","journal-title":"Grana"},{"key":"B48","doi-asserted-by":"publisher","first-page":"9","DOI":"10.3897\/phytokeys.19.3912","article-title":"Chilean Pitavia more closely related to Oceania and old world rutaceae than to Neotropical groups: Evidence from two cpDNA non-coding regions, with a new subfamilial classification of the family","volume":"19","author":"Groppo","year":"2012","journal-title":"Phytokeys"},{"key":"B49","doi-asserted-by":"publisher","first-page":"985","DOI":"10.3732\/ajb.2007313","article-title":"Phylogeny of rutaceae based on two noncoding regions from cpDNA","volume":"95","author":"Groppo","year":"2008","journal-title":"Am. J. Bot."},{"key":"B50","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1007\/s40415-021-00728-6","article-title":"Chromosome numbers and their evolutionary meaning in the sapindales order: An overview","volume":"45","author":"Guimar\u00e3es","year":"2022","journal-title":"Braz. J. Bot."},{"key":"B51","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1600\/0363644054223549","article-title":"Phylogenetic inference in sapindaceae sensu lato using plastid matK and rbcL DNA sequences","volume":"30","author":"Harrington","year":"2005","journal-title":"Syst. Bot."},{"key":"B52","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1007\/s11430-016-0095-9","article-title":"Toward understanding Cretaceous climate\u2013an updated review","volume":"60","author":"Hay","year":"2017","journal-title":"Sci. China Earth Sci."},{"key":"B53","doi-asserted-by":"publisher","first-page":"479","DOI":"10.1086\/703551","article-title":"19-Million-Year-Old spondioid fruits from Panama reveal a dynamic dispersal history for anacardiaceae","volume":"180","author":"Herrera","year":"2019","journal-title":"Int. J. Plant Sci."},{"key":"B54","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1016\/j.revpalbo.2012.02.007","article-title":"Permineralized fruits from the late Eocene of Panama give clues of the composition of forests established early in the uplift of central America","volume":"175","author":"Herrera","year":"2012","journal-title":"Rev. Palaeobot. Palynol."},{"key":"B55","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1007\/s12229-018-9201-1","article-title":"Fruit morphology and anatomy of the spondioid anacardiaceae","volume":"84","author":"Herrera","year":"2018","journal-title":"Bot. Rev."},{"key":"B56","doi-asserted-by":"publisher","article-title":"Polyploidy: its consequences and enabling role in plant diversification and evolution","author":"Heslop-Harrison","year":"2022","journal-title":"Ann. Bot.","DOI":"10.1093\/aob\/mcac132"},{"key":"B57","doi-asserted-by":"publisher","first-page":"718","DOI":"10.1126\/science.189.4204.718","article-title":"Lepidopteran leaf mine from the early Eocene wind river formation of northwestern Wyoming","volume":"189","author":"Hickey","year":"1975","journal-title":"Science"},{"key":"B58","doi-asserted-by":"publisher","first-page":"518","DOI":"10.1093\/molbev\/msx281","article-title":"UFBoot2: Improving the ultrafast bootstrap approximation","volume":"35","author":"Hoang","year":"2018","journal-title":"Mol. Biol. Evol."},{"key":"B59","volume-title":"The families of flowering plants arranged according to a new system based on their probable phylogeny","author":"Hutchinson","year":"1926"},{"key":"B60","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1038\/nature09916","article-title":"Ancestral polyploidy in seed plants and angiosperms","volume":"473","author":"Jiao","year":"2011","journal-title":"Nature"},{"key":"B61","doi-asserted-by":"publisher","DOI":"10.3732\/apps.1600016","article-title":"HybPiper: Extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment","volume":"4","author":"Johnson","year":"2016","journal-title":"App. Plant Sci."},{"key":"B62","doi-asserted-by":"publisher","first-page":"594","DOI":"10.1093\/sysbio\/syy086","article-title":"A universal probe set for targeted sequencing of 353 nuclear genes from any flowering plant designed using k-medoids clustering","volume":"68","author":"Johnson","year":"2019","journal-title":"Syst. Biol."},{"key":"B63","doi-asserted-by":"publisher","first-page":"e11295","DOI":"10.1002\/aps3.11295","article-title":"An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in asteraceae","volume":"7","author":"Jones","year":"2019","journal-title":"App. Plant Sci."},{"key":"B64","doi-asserted-by":"publisher","first-page":"1669","DOI":"10.1093\/bioinformatics\/btq243","article-title":"The newick utilities: high-throughput phylogenetic tree processing in the Unix shell","volume":"26","author":"Junier","year":"2010","journal-title":"Bioinformatics"},{"key":"B65","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: Fast model selection for accurate phylogenetic estimates","volume":"14","author":"Kalyaanamoorthy","year":"2017","journal-title":"Nat. Methods"},{"key":"B66","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"B67","volume-title":"Monographie der fr\u00fcchte und samen in der kreide von mitteleuropa","author":"Knobloch","year":"1986"},{"key":"B68","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1111\/nph.13490","article-title":"Recently evolved diversity and convergent radiations of rainforest mahoganies (Meliaceae) shed new light on the origins of rainforest hyperdiversity","volume":"207","author":"Koenen","year":"2015","journal-title":"New Phytol."},{"key":"B69","doi-asserted-by":"crossref","volume-title":"Flowering plants. eudicots: Sapindales, cucurbitales, myrtaceae","author":"Kubitzki","year":"2011","DOI":"10.1007\/978-3-642-14397-7"},{"key":"B70","doi-asserted-by":"publisher","first-page":"1695","DOI":"10.1093\/molbev\/mss020","article-title":"PartitionFinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses","volume":"29","author":"Lanfear","year":"2012","journal-title":"Mol. Biol. Evol."},{"key":"B71","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2019.01655","article-title":"Tackling rapid radiations with targeted sequencing","volume":"10","author":"Larridon","year":"2020","journal-title":"Front. Plant Sci."},{"key":"B72","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12915-021-01166-2","article-title":"Plastid phylogenomic insights into relationships of all flowering plant families","volume":"19","author":"Li","year":"2021","journal-title":"BMC Biol."},{"key":"B73","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1038\/s41477-019-0421-0","article-title":"Origin of angiosperms and the puzzle of the Jurassic gap","volume":"5","author":"Li","year":"2019","journal-title":"Nat. Plants"},{"key":"B74","doi-asserted-by":"publisher","first-page":"e1040","DOI":"10.1002\/aps3.1040","article-title":"Complete plastome sequencing from Toona (Meliaceae) and phylogenomic analyses within sapindales","volume":"6","author":"Lin","year":"2018","journal-title":"Appl. Plant Sci."},{"key":"B75","volume-title":"Fossil plants of the florissant beds, Colorado","author":"MacGinitie","year":"1953"},{"key":"B76","volume-title":"The Eocene green river flora of northwestern Colorado and northeastern Utah","author":"MacGinitie","year":"1969"},{"key":"B77","doi-asserted-by":"publisher","first-page":"437","DOI":"10.1111\/nph.13264","article-title":"A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity","volume":"207","author":"Magall\u00f3n","year":"2015","journal-title":"New Phytol."},{"key":"B78","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1186\/s12864-018-4620-2","article-title":"TreeShrink: Fast and accurate detection of outlier long branches in collections of phylogenetic trees","volume":"19","author":"Mai","year":"2018","journal-title":"BMC Genom."},{"key":"B79","doi-asserted-by":"publisher","first-page":"985","DOI":"10.1086\/320783","article-title":"Leaves and fruits of Aesculus (Sapindales) from the Paleocene of north America","volume":"162","author":"Manchester","year":"2001","journal-title":"Int. J. Plant Sci."},{"key":"B80","first-page":"137","article-title":"Update on the megafossil flora of florissant, Colorado","volume-title":"Fossil flora and stratigraphy of the florissant formation, Colorado","author":"Manchester","year":"2001"},{"key":"B81","first-page":"7","article-title":"Late Eocene silicified fruits and seeds from the John day formation near post, Oregon","volume":"27","author":"Manchester","year":"2007","journal-title":"PaleoBios"},{"key":"B82","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s12229-010-9041-0","article-title":"Phylogenetic distribution and identification of fin-winged fruits","volume":"76","author":"Manchester","year":"2010","journal-title":"Bot. Rev."},{"key":"B83","doi-asserted-by":"publisher","first-page":"1199","DOI":"10.1086\/520728","article-title":"Fossil cashew nuts from the Eocene of Europe: Biogeographic links between Africa and south America","volume":"168","author":"Manchester","year":"2007","journal-title":"Int. J. Plant Sci."},{"key":"B84","doi-asserted-by":"publisher","first-page":"1316","DOI":"10.2307\/3558343","article-title":"Dipteronia (Sapindaceae) from the tertiary of north America and implications for the phytogeographic history of the aceroideae","volume":"88","author":"McClain","year":"2001","journal-title":"Am. J. Bot."},{"key":"B85","doi-asserted-by":"publisher","DOI":"10.1002\/aps3.11443","article-title":"Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics","volume":"9","author":"McDonnell","year":"2021","journal-title":"Appl. Plant Sci."},{"key":"B86","doi-asserted-by":"publisher","DOI":"10.1002\/aps3.11420","article-title":"New targets acquired: Improving locus recovery from the Angiosperms353 probe set","volume":"9","author":"McLay","year":"2021","journal-title":"Appl. Plant Sci."},{"key":"B87","volume-title":"The oligocene bridge creek flora of the John day formation, Oregon","author":"Meyer","year":"1997"},{"key":"B88","doi-asserted-by":"publisher","first-page":"i541","DOI":"10.1093\/bioinformatics\/btu462","article-title":"ASTRAL: genome-scale coalescent-based species tree estimation","volume":"30","author":"Mirarab","year":"2014","journal-title":"Bioinformatics"},{"key":"B89","volume-title":"The cashew and its relatives (Anacardium: Anacardiaceae)","author":"Mitchell","year":"1987"},{"key":"B90","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1600\/036364406777585757","article-title":"Poupartiopsis gen. nov. and its context in anacardiaceae classification","volume":"31","author":"Mitchell","year":"2006","journal-title":"Syst. Bot."},{"key":"B91","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1007\/s40415-022-00793-5","article-title":"Neotropical Anacardiaceae (cashew family)","volume":"45","author":"Mitchell","year":"2022","journal-title":"Braz. J. Bot."},{"key":"B92","doi-asserted-by":"publisher","DOI":"10.1093\/sysbio\/syab032","article-title":"Analysis of paralogs in target enrichment data pinpoints multiple ancient polyploidy events in alchemilla s.l. (Rosaceae)","volume":"71","author":"Morales-Briones","year":"2021","journal-title":"Syst. Biol."},{"key":"B93","doi-asserted-by":"publisher","first-page":"98","DOI":"10.2307\/25065951","article-title":"An evaluation of tribes and generic relationships in melioideae (Meliaceae) based on nuclear ITS ribosomal DNA","volume":"57","author":"Muellner","year":"2008","journal-title":"Taxon"},{"key":"B94","doi-asserted-by":"publisher","first-page":"471","DOI":"10.3732\/ajb.90.3.471","article-title":"Molecular phylogenetics of meliaceae (Sapindales) based on nuclear and plastid DNA sequences","volume":"90","author":"Muellner","year":"2003","journal-title":"Am. J. Bot."},{"key":"B95","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1016\/j.ympev.2006.03.001","article-title":"The mahogany family \u201cout-of-Africa\u201d: Divergence time estimation, global biogeographic patterns inferred from plastid rbcL DNA sequences, extant, and fossil distribution of diversity","volume":"40","author":"Muellner","year":"2006","journal-title":"Mol. Phylogenet. Evol."},{"key":"B96","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1007\/s00606-007-0546-x","article-title":"Placing biebersteiniaceae, a herbaceous clade of sapindales, in a temporal and geographic context","volume":"266","author":"Muellner","year":"2007","journal-title":"Plant Syst. Evol."},{"key":"B97","doi-asserted-by":"publisher","first-page":"1019","DOI":"10.12705\/655.5","article-title":"Molecular phylogenetics and molecular clock dating of sapindales based on plastid rbcL, atpB and trnL-trnF DNA sequences","volume":"65","author":"Muellner-Riehl","year":"2016","journal-title":"Taxon"},{"key":"B98","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1002\/aps3.11441","article-title":"HybPhaser: A workflow for the detection and phasing of hybrids in target capture data sets","volume":"9","author":"Nauheimer","year":"2021","journal-title":"App. Plant Sci."},{"key":"B99","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"B100","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1007\/s40415-021-00764-2","article-title":"The wood anatomy of sapindales: Diversity and evolution of wood characters","volume":"45","author":"Pace","year":"2022","journal-title":"Braz. J. Bot."},{"key":"B101","doi-asserted-by":"publisher","first-page":"621","DOI":"10.1111\/jse.12454","article-title":"The odd one out or a hidden generalist: Hawaiian Melicope (Rutaceae) do not share traits associated with successful island colonization","volume":"56","author":"Paetzold","year":"2018","journal-title":"J. Syst. Evol."},{"key":"B102","doi-asserted-by":"publisher","first-page":"188","DOI":"10.1016\/j.revpalbo.2009.12.005","article-title":"Rutaceae leaf fossils from the late oligocene (27.23 ma) guang river flora of northwestern Ethiopia","volume":"159","author":"Pan","year":"2010","journal-title":"Rev. Palaeobot. Palynol."},{"key":"B103","doi-asserted-by":"publisher","first-page":"2294","DOI":"10.1104\/pp.16.00523","article-title":"Evolution of gene duplication in plants","volume":"171","author":"Panchy","year":"2016","journal-title":"Plant Physiol."},{"key":"B104","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1080\/08912963.2018.1487421","article-title":"Fossil leaves of subtropical lineages in the Eocene\u2013?Oligocene of southern Patagonia","volume":"32","author":"Panti","year":"2020","journal-title":"Hist. Biol."},{"key":"B105","doi-asserted-by":"publisher","first-page":"346","DOI":"10.1093\/sysbio\/syr107","article-title":"Best practices for justifying fossil calibrations","volume":"61","author":"Parham","year":"2012","journal-title":"Syst. Biol."},{"key":"B106","volume-title":"Molecular systematics of the cashew family (Anacardiaceae)","author":"Pell","year":"2004"},{"key":"B107","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1600\/036364408784571545","article-title":"Phylogenetic split of Malagasy and African taxa of Protorhus and Rhus (Anacardiaceae) based on cpDNA trnL-trnF and nrDNA ETS and ITS sequence data","volume":"33","author":"Pell","year":"2008","journal-title":"Syst. Bot."},{"key":"B108","first-page":"7","article-title":"Anacardiaceae","volume-title":"The families and genera of vascular plants. eudicots: Sapindales, cucurbitales, myrtaceae","author":"Pell","year":"2011"},{"key":"B109","first-page":"419","article-title":"A generic monograph of the meliaceae","volume":"22","author":"Pennington","year":"1975","journal-title":"Blumea"},{"key":"B110","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1007\/s40415-021-00731-x","article-title":"An updated account of simaroubaceae with emphasis on American taxa","volume":"45","author":"Pirani","year":"2022","journal-title":"Braz. J. Bot."},{"key":"B111","article-title":"Sapindaceae","volume-title":"Das pflanzenreich","author":"Radlkofer","year":"1931"},{"key":"B112","doi-asserted-by":"publisher","first-page":"901","DOI":"10.1093\/sysbio\/syy032","article-title":"Posterior summarization in Bayesian phylogenetics using tracer 1.7","volume":"67","author":"Rambaut","year":"2018","journal-title":"Syst. Biol."},{"key":"B113","doi-asserted-by":"publisher","first-page":"1232","DOI":"10.1038\/s41559-020-1241-3","article-title":"The delayed and geographically heterogeneous diversification of flowering plant families","volume":"4","author":"Ram\u00edrez-Barahona","year":"2020","journal-title":"Nat. Ecol. Evol."},{"key":"B114","doi-asserted-by":"crossref","volume-title":"The London clay flora","author":"Reid","year":"1933","DOI":"10.5962\/bhl.title.110147"},{"key":"B115","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1007\/s40415-021-00723-x","article-title":"A comprehensive review of the chemical composition and epicuticular wax morphology of the cuticle in sapindales","volume":"45","author":"Roma","year":"2022","journal-title":"Braz. J. Bot."},{"key":"B116","doi-asserted-by":"publisher","first-page":"3840","DOI":"10.1093\/jxb\/erac130","article-title":"What is the age of flowering plants","volume":"73","author":"Sauquet","year":"2022","journal-title":"J. Exp. Bot."},{"key":"B117","doi-asserted-by":"publisher","first-page":"306","DOI":"10.1093\/sysbio\/49.2.306","article-title":"Phylogenetics of flowering plants based on combined analysis of plastid atpB and rbcL gene sequences","volume":"49","author":"Savolainen","year":"2000","journal-title":"Syst. Biol."},{"key":"B118","doi-asserted-by":"publisher","first-page":"2048","DOI":"10.3732\/ajb.0900086","article-title":"Tertiary leaf fossils of Mangifera (Anacardiaceae) from Li basin, Thailand as examples of the utility of leaf marginal venation characters","volume":"96","author":"Sawangchote","year":"2009","journal-title":"Am. J. Bot."},{"key":"B119","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1146\/annurev-earth-081320-064052","article-title":"An atlas of phanerozoic paleogeographic maps: The seas come in and the seas go out","volume":"49","author":"Scotese","year":"2021","journal-title":"Annu. Rev. Earth Planet Sci."},{"key":"B120","doi-asserted-by":"crossref","article-title":"Fossil data support a pre-Cretaceous origin of flowering plants","volume-title":"Nature Ecology & Evolution","author":"Silvestro","year":"2021","DOI":"10.1038\/s41559-020-01387-8"},{"key":"B121","first-page":"39","article-title":"The economic complexity observatory: An analytical tool for understanding the dynamics of economic development","volume-title":"Scalable integration of analytics and visualization: Papers from the 2011 AAAI workshop","author":"Simoes","year":"2011"},{"key":"B122","unstructured":"SimoesA. J. G.\n HidalgoC. A.\n OEC 5.0, the observatory of economic complexity2022"},{"key":"B123","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1016\/j.tig.2020.08.012","article-title":"New approaches for inferring phylogenies in the presence of paralogs","volume":"37","author":"Smith","year":"2021","journal-title":"Trends Genet."},{"key":"B124","doi-asserted-by":"publisher","first-page":"e0197433","DOI":"10.1371\/journal.pone.0197433","article-title":"So many genes, so little time: A practical approach to divergence-time estimation in the genomic era","volume":"13","author":"Smith","year":"2018","journal-title":"PloS One"},{"key":"B125","doi-asserted-by":"publisher","first-page":"715","DOI":"10.1093\/bioinformatics\/btm619","article-title":"Phyutility: A phyloinformatics tool for trees, alignments and molecular data","volume":"24","author":"Smith","year":"2008","journal-title":"Bioinformatics"},{"key":"B126","doi-asserted-by":"publisher","first-page":"336","DOI":"10.3732\/ajb.0800079","article-title":"Polyploidy and angiosperm diversification","volume":"96","author":"Soltis","year":"2009","journal-title":"Am. J. Bot."},{"key":"B127","unstructured":"StevensP. F.\n Angiosperm phylogeny website version 142001"},{"key":"B128","doi-asserted-by":"crossref","first-page":"7","volume-title":"Flowering plants: Class magnoliopsida (Dicotyledons)","author":"Takhtajan","year":"2009","DOI":"10.1007\/978-1-4020-9609-9_2"},{"key":"B129","volume-title":"Wood anatomy of the anacardiaceae: ecological and phylogenetic interpretation","author":"Terrazas","year":"1994"},{"key":"B130","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1007\/BF02988138","article-title":"Euodia costata (Chandler) tiffney, (Rutaceae) from the Eocene of southern England","volume":"55","author":"Tiffney","year":"1981","journal-title":"Pal\u00e4ontol. Z."},{"key":"B131","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1007\/s40415-021-00778-w","article-title":"Diversity and evolution of secretory structures in sapindales","volume":"45","author":"T\u00f6lke","year":"2022","journal-title":"Braz. J. Bot."},{"key":"B132","doi-asserted-by":"publisher","first-page":"3018","DOI":"10.1111\/1755-0998.13684","article-title":"Utilizing paralogs for phylogenetic reconstruction has the potential to increase species tree support and reduce gene tree discordance in target enrichment data","volume":"22","author":"Ufimov","year":"2022","journal-title":"Mol. Ecol. Res."},{"key":"B133","doi-asserted-by":"publisher","first-page":"3853","DOI":"10.1073\/pnas.0813376106","article-title":"Rosid radiation and the rapid rise of angiosperm-dominated forests","volume":"106","author":"Wang","year":"2009","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B134","doi-asserted-by":"publisher","first-page":"422","DOI":"10.3732\/ajb.1200415","article-title":"Fruits of Koelreuteria (Sapindaceae) from the Cenozoic throughout the northern hemisphere: their ecological, evolutionary, and biogeographic implications","volume":"100","author":"Wang","year":"2013","journal-title":"Am. J. Bot."},{"key":"B135","volume-title":"Systematics of the anacardiaceae and its allies","author":"Wannan","year":"1986"},{"key":"B136","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1111\/j.1095-8339.1990.tb01878.x","article-title":"Pericarp structure and generic affinities in the anacardiaceae","volume":"102","author":"Wannan","year":"1990","journal-title":"Bot. J. Linn. Soc"},{"key":"B137","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1111\/j.1095-8339.1991.tb00228.x","article-title":"Floral structure and evolution in the anacardiaceae","volume":"107","author":"Wannan","year":"1991","journal-title":"Bot. J. Linn. Soc"},{"key":"B138","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1016\/0305-1978(85)90066-3","article-title":"Biflavonyls and the affinities of Blepharocarya","volume":"13","author":"Wannan","year":"1985","journal-title":"Biochem. Syst. Ecol."},{"key":"B139","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1007\/978-1-4899-1783-6_9","article-title":"Phytochemical diversity in the order rutales","volume-title":"Phytochemical potential of tropical plants","author":"Waterman","year":"1993"},{"key":"B140","doi-asserted-by":"publisher","first-page":"2896","DOI":"10.1016\/j.phytochem.2007.06.029","article-title":"The current status of chemical systematics","volume":"68","author":"Waterman","year":"2007","journal-title":"Phytochemistry"},{"key":"B141","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2014.00409","article-title":"To move or to evolve: Contrasting patterns of intercontinental connectivity and climatic niche evolution in \u201cTerebinthaceae\u201d (Anacardiaceae and burseraceae)","volume":"5","author":"Weeks","year":"2014","journal-title":"Front. Genet."},{"key":"B142","volume-title":"Handbuch der systematischen botanik","author":"Wettstein","year":"1901"},{"key":"B143","doi-asserted-by":"publisher","first-page":"1201","DOI":"10.1086\/671796","article-title":"Citrus linczangensis sp. n., a leaf fossil of rutaceae from the late Miocene of yunnan, China","volume":"174","author":"Xie","year":"2013","journal-title":"Int. J. Plant Sci."},{"key":"B144","doi-asserted-by":"publisher","first-page":"2004","DOI":"10.1111\/1755-6724.13692","article-title":"Mid-Cretaceous hothouse climate and the expansion of early angiosperms","volume":"92","author":"Zhang","year":"2018","journal-title":"Acta Geol. Sin."}],"container-title":["Frontiers in Plant Science"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpls.2023.1063174\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,3,7]],"date-time":"2023-03-07T05:49:14Z","timestamp":1678168154000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpls.2023.1063174\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,3,7]]},"references-count":144,"alternative-id":["10.3389\/fpls.2023.1063174"],"URL":"http:\/\/dx.doi.org\/10.3389\/fpls.2023.1063174","relation":{},"ISSN":["1664-462X"],"issn-type":[{"value":"1664-462X","type":"electronic"}],"subject":["Plant Science"],"published":{"date-parts":[[2023,3,7]]}}} |