References
- Andrews, S, P Lindenbaum, B Howard, P Ewels 2010. FastQC: a quality control tool for high throughput sequence data. Available online at http:/www.bioinformatics.babraham.ac.uk/projects/fastqc
- Baguette, M, JAM Bertrand, V Stevens, B Schatz, C Noûs. 2020. Why are there so many Bee-orchids? Adaptive radiation by intraspecific competition for mnemonic pollinators. Biol Rev. 95:1630–1663. doi:https://doi.org/10.1111/brv.12633.
- Bateman, RM. 2018. Two bees or not two bees? An overview of Ophrys systematics. Ber Aus Arbeitkreisen Heimische Orchideen. 35:5–46.
- Bateman, RM, G Sramkó, O Paun. 2018. Integrating restriction site-associated DNA sequencing (RAD-seq) with morphological cladistics analysis clarifies evolutionary relationships among major species groups of bee orchids. Ann Bot. 121:85–105. doi:https://doi.org/10.1093/aob/mcx129.
- Bertrand, JAM, M Baguette, N Joffard, B Schatz. 2021. Challenges inherent in the systematics and taxonomy of genera that have recently experienced explosive radiation: the case of orchids of the genus Ophrys. In M C Maugin, P Grandcolas, editors. Systematics and exploration of life. Paris: ISTE.
- Bertrand, JAM, A Gibert, C Llauro, O Panaud. 2019. Characterization of the complete plastome of Ophrys aveyronensis, Euro-Mediterranean orchid with an intriguing disjunct geographic distribution. Mitochondrial DNA Part B. 4:3256–3257. doi:https://doi.org/10.1080/23802359.2019.1670748.
- Bolger, AM, M Lohse, B Usadel. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30:2114–2120. doi:https://doi.org/10.1093/bioinformatics/btu170.
- Breitkopf, H, RE Onstein, D Cafasso, PM Schlüter, S Cozzolino. 2015. Multiple shifts between different pollinators fueled rapid diversification in sexually deceptive Ophrys orchids. New Phytol. 207:377–386. doi:https://doi.org/10.1111/nph.13219.
- Devey, DS, RM Bateman, MF Fay, JA Hawkins. 2008. Friends or realtives? Phylogenetics and species delimitation in the controversial European orchid genus Ophrys. Ann Bot. 101:385–402. doi:https://doi.org/10.1093/aob/mcm299.
- Dierckxsens, N, P Mardulyn, G Smits. 2017. NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Res. 45:e18. doi:https://doi.org/10.1093/nar/gkw955.
- Givnish, TJ, D Spalink, M Ames, SP Lyon, SJ Hunter, A Zuluaga, WJD Iles, MA Clements, MTK Arroyo, J Leebens-Mack, et al. 2015. Orchid phylogenomics and multiple drivers of their extraordinary diversification. Proc R Soc B. 282:20151553. doi:https://doi.org/10.1098/rspb.2015.1553.
- Gonçalves, DJP, BB Simpson, EM Ortiz, GH Shimizu, RK Jansen. 2019. Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes. Mol Phylogenet Evol. 138:219–232. doi:https://doi.org/10.1016/j.ympev.2019.05.022.
- Langmead, B, SL Salzberg. 2012. Fast gapped-read alignment with bowtie 2. Nat Methods. 9:357–359. doi:https://doi.org/10.1038/nmeth.1923
- Li, H. 2018. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 34:3094–3100. doi:https://doi.org/10.1093/bioinformatics/bty191.
- Minh, BQ, HA Schmidt, O Chernomor, MD Schrempf, A Woodhams, A Von Haeseler, R Lanfear. 2020b. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 37:1510–1534.
- Minh, BQ, MW Hahn, R Lanfear. 2020a. New methods to calculate concordance factors for phylogenomic datasets. Mol Biol Evol. 37:2727–2733. doi:https://doi.org/10.1093/molbev/msaa106.
- Piñeiro Fernández, L, KJRP Byers, J Cai, KME Seedeek, RT Kellenberger, A Russo, W Qi, C Aquino Fournier, PM Schlüter. 2019. A phylogenomic analysis of the floral transcriptomes of sexually deceptive and rewarding European orchids, Ophrys and Gymnadenia. Front Plant Sci. 10:1553. doi:https://doi.org/10.3389/fpls.2019.01553.
- Roma, L, S Cozzolino, PM Schlüter, G Scopece, D Cafasso. 2018. The complete plastid genomes of Ophrys iricolor and O. sphegodes (Orchidaceae) and comparative analyses with other orchids. PLoS One. 13:e0204174. doi:https://doi.org/10.1371/journal.pone.0204174.
- Scheunert, A, M Dorfner, T Lingl, C Oberprieler. 2020. Can we use it? On the utility of de novo and reference-based assembly of Nanopore data for plant plastome sequencing. PLoS One. 15:e0226234. doi:https://doi.org/10.1371/journal.pone.0226234.
- Shen, -X-X, CT Hittinger, A Rokas. 2017. Contentions relationships in phylogenomic studies can be driven by a handful of genes. Nat Ecol Evol. 1:0126. doi:https://doi.org/10.1038/s41559-017-0126.
- Soliva, M, A Kocyan, A Widmer. 2001. Molecular phylogenetics of the sexually deceptive orchid genus Ophrys (Orchidaceae) based on nuclear and chloroplast DNA sequences. Mol Phylogenet Evol. 20:78–88. doi:https://doi.org/10.1006/mpev.2001.0953.
- Tyteca, D, M Baguette. 2017. Ophrys (Orchidaceae) systematics – when molecular phylogenetics, morphology and biology reconcile. Ber Aus Arbeitkreisen Heimische Orchideen. 34:37–103.
- Walker, JF, N Walker-Hale, OM Vargas, DA Larson, GW Stull. 2019. Characterizing gene tree conflict in plastome-inferred phylogenies. PeerJ. 7:e7747. doi:https://doi.org/10.7717/peerj.7747.
- Wang, W, M Schalamun, A Morales-Suarez, D Kainer, B Schwessinger, R Lanfear. 2018. Assembly of chloroplast genomes with long- and short read data: a comparison of approaches using Eucalyptus pauciflora as a test. BMC Genomics. 19:977. doi:https://doi.org/10.1186/s12864-018-5348-8.
- Wick, RR, LM Judd, CL Gorrie, KE Holt. 2017. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 13:e1005595. doi:https://doi.org/10.1371/journal.pcbi.1005595.