References
Barton, N. H. (1980). The fitness of hybrids between two chromosomal races of the grasshopper Podisma pedestris . Heredity ,45 (1), 47–59. doi:10.1038/hdy.1980.49
Barton, N. H., & Hewitt, G. M. (1981). The genetic basis of hybrid inviability in the grasshopper Podisma pedestris .Heredity , 47 (3), 367–383. doi:10.1038/hdy.1981.98
Bates, D., Mächler, M., Bolker, B., & Walker, S. (2015). Fitting linear mixed-effects models using lme4. Journal of Statistical Software ,67 (1), 1–48. doi:10.18637/jss.v067.i01
Bensasson, D., Petrov, D. A., Zhang, D.-X., Hartl, D. L., & Hewitt, G. M. (2001). Genomic gigantism: DNA loss is slow in mountain grasshoppers.Molecular Biology and Evolution , 18 (2), 246–253. doi:10.1093/oxfordjournals.molbev.a003798
Bensasson, D., Zhang, D.-X., Hartl, D. L., & Hewitt, G. M. (2001). Mitochondrial pseudogenes: evolution’s misplaced witnesses. Trends in Ecology & Evolution , 16 (6), 314–321. doi:10.1016/S0169-5347(01)02151-6
Bensasson, D., Zhang, D.-X., & Hewitt, G. M. (2000). Frequent assimilation of mitochondrial DNA by grasshopper nuclear genomes.Molecular Biology and Evolution , 17 (3), 406–415. doi:10.1093/oxfordjournals.molbev.a026320
Bernt, M., Donath, A., Jühling, F., Externbrink, F., Florentz, C., Fritzsch, G., … Stadler, P. F. (2013). MITOS: Improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics and Evolution , 69 (2), 313–319. doi:10.1016/j.ympev.2012.08.023
Boore, J. L. (1999). Animal mitochondrial genomes. Nucleic Acids Research , 27 (8), 1767–1780. doi:10.1093/nar/27.8.1767
Brower, A. V. (1994). Rapid morphological radiation and convergence among races of the butterfly Heliconius erato inferred from patterns of mitochondrial DNA evolution. Proceedings of the National Academy of Sciences , 91 (14), 6491 LP – 6495. doi:10.1073/pnas.91.14.6491
Cheng, S., Melkonian, M., Smith, S. A., Brockington, S., Archibald, J. M., Delaux, P.-M., … Wong, G. K.-S. (2018). 10KP: A phylodiverse genome sequencing plan. GigaScience , 7 (3), giy013. doi:10.1093/gigascience/giy013
Dierckxsens, N., Mardulyn, P., & Smits, G. (2016). NOVOPlasty: de novo assembly of organelle genomes from whole genome data.Nucleic Acids Research , 45 (4), gkw955. doi:10.1093/nar/gkw955
Dodsworth, S., Chase, M. W., Kelly, L. J., Leitch, I. J., Macas, J., Novák, P., … Leitch, A. R. (2015). Genomic repeat abundances contain phylogenetic signal. Systematic Biology , 64 (1). doi:10.1093/sysbio/syu080
Doležel, J., Bartoš, J., Voglmayr, H., & Greilhuber, J. (2003). Letter to the editor. Cytometry , 51A (2), 127–128. doi:10.1002/cyto.a.10013
Hawlitschek, O., Morinière, J., Lehmann, G. U. C., Lehmann, A. W., Kropf, M., Dunz, A., … Haszprunar, G. (2017). DNA barcoding of crickets, katydids and grasshoppers (Orthoptera) from Central Europe with focus on Austria, Germany and Switzerland. Molecular Ecology Resources , 17 (5), 1037–1053. doi:10.1111/1755-0998.12638
Hazkani-Covo, E., Zeller, R. M., & Martin, W. (2010). Molecular poltergeists: Mitochondrial DNA copies (numts) in sequenced nuclear genomes. PLoS Genetics , 6 (2), e1000834. doi:10.1371/journal.pgen.1000834
Hewitt, G. M., & John, B. (1972). Inter-population sex chromosome polymorphism in the grasshopper Podisma pedestris .Chromosoma , 37 (1), 23–42. doi:10.1007/BF00329555
Hotopp, J. C. D., Clark, M. E., Oliveira, D. C. S. G., Foster, J. M., Fischer, P., Torres, M. C. M., … Werren, J. H. (2007). Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science , 317 (5845), 1753 LP – 1756. doi:10.1126/science.1142490
Jin, J.-J., Yu, W.-B., Yang, J.-B., Song, Y., dePamphilis, C. W., Yi, T.-S., & Li, D.-Z. (2020). GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biology , 21 (1), 241. doi:10.1186/s13059-020-02154-5
John, B., & Hewitt, G. M. (1970). Inter-population sex chromosome polymorphism in the grasshopper Podisma pedestris .Chromosoma , 31 (3), 291–308. doi:10.1007/BF00321226
Kolodner, R., & Tewari, K. K. (1979). Inverted repeats in chloroplast DNA from higher plants. Proceedings of the National Academy of Sciences , 76 (1), 41 LP – 45. doi:10.1073/pnas.76.1.41
Lansman, R. A., Shade, R. O., Shapira, J. F., & Avise, J. C. (1981). The use of restriction endonucleases to measure mitochondrial DNA sequence relatedness in natural populations. Journal of Molecular Evolution , 17 (4), 214–226.
Lewin, H. A., Robinson, G. E., Kress, W. J., Baker, W. J., Coddington, J., Crandall, K. A., … Zhang, G. (2018). Earth BioGenome Project: Sequencing life for the future of life. Proceedings of the National Academy of Sciences , 115 (17), 4325 LP – 4333. doi:10.1073/pnas.1720115115
Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics , 25 (14), 1754–1760. doi:10.1093/bioinformatics/btp324
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., … Subgroup, 1000 Genome Project Data Processing. (2009). The sequence alignment/map format and SAMtools. Bioinformatics ,25 (16), 2078–2079. doi:10.1093/bioinformatics/btp352
Li, W., Freudenberg, J., & Freudenberg, J. (2019). Alignment-free approaches for predicting novel nuclear mitochondrial segments (NUMTs) in the human genome. Gene , 691 , 141–152. doi:https://doi.org/10.1016/j.gene.2018.12.040
Liang, B., Wang, N., Li, N., Kimball, R. T., & Braun, E. L. (2018). Comparative genomics reveals a burst of homoplasy-free numt insertions.Molecular Biology and Evolution , 35 (8), 2060–2064. doi:10.1093/molbev/msy112
Lopez, J. V., Yuhki, N., Masuda, R., Modi, W., & O’Brien, S. J. (1994). Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat. Journal of Molecular Evolution , 39 (2), 174–190. doi:10.1007/BF00163806
Macher, J.-N., Zizka, V. M. A., Weigand, A. M., & Leese, F. (2018). A simple centrifugation protocol for metagenomic studies increases mitochondrial DNA yield by two orders of magnitude. Methods in Ecology and Evolution , 9 (4), 1070–1074. doi:https://doi.org/10.1111/2041-210X.12937
McElroy, K., Beattie, K., Symonds, M. R. E., & Joseph, L. (2018). Mitogenomic and nuclear diversity in the mulga parrot of the Australian arid zone: cryptic subspecies and tests for selection. Emu - Austral Ornithology , 118 (1), 22–35. doi:10.1080/01584197.2017.1411765
Mower, J. P., Sloan, D. B., & Alverson, A. J. (2012). Plant Mitochondrial Genome Diversity: The Genomics Revolution BT - Plant Genome Diversity Volume 1: Plant Genomes, their Residents, and their Evolutionary Dynamics. In J. F. Wendel, J. Greilhuber, J. Dolezel, & I. J. Leitch (Eds.) (pp. 123–144). Vienna: Springer Vienna. doi:10.1007/978-3-7091-1130-7_9
Nacer, D. F., & Raposo do Amaral, F. (2017). Striking pseudogenization in avian phylogenetics: Numts are large and common in falcons.Molecular Phylogenetics and Evolution , 115 , 1–6. doi:https://doi.org/10.1016/j.ympev.2017.07.002
Naciri, Y., & Manen, J.-F. (2010). Potential DNA transfer from the chloroplast to the nucleus in Eryngium alpinum . Molecular Ecology Resources , 10 (4), 728–731. doi:https://doi.org/10.1111/j.1755-0998.2009.02816.x
Nichols, R. A., & Hewitt, G. M. (1988). Genetical and ecological differentiation across a hybrid zone. Ecological Entomology ,13 (1), 39–49. doi:10.1111/j.1365-2311.1988.tb00331.x
Nikoh, N., McCutcheon, J. P., Kudo, T., Miyagishima, S., Moran, N. A., & Nakabachi, A. (2010). Bacterial genes in the aphid genome: Absence of functional gene transfer from Buchnera to its host. PLOS Genetics , 6 (2), e1000827. Retrieved from https://doi.org/10.1371/journal.pgen.1000827
Pereira, S. L., & Baker, A. J. (2004). Low number of mitochondrial pseudogenes in the chicken (Gallus gallus ) nuclear genome: Implications for molecular inference of population history and phylogenetics. BMC Evolutionary Biology , 4 (1), 17. doi:10.1186/1471-2148-4-17
Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., … Jarvis, E. D. (2021). Towards complete and error-free genome assemblies of all vertebrate species. Nature ,592 (7856), 737–746. doi:10.1038/s41586-021-03451-0
Ricchetti, M., Tekaia, F., & Dujon, B. (2004). Continued Colonization of the Human Genome by Mitochondrial DNA. PLOS Biology ,2 (9), e273. Retrieved from https://doi.org/10.1371/journal.pbio.0020273
Richly, E., & Leister, D. (2004). NUMTs in sequenced eukaryotic genomes. Molecular Biology and Evolution , 21 (6), 1081–4. doi:10.1093/molbev/msh110
Ross, M. G., Russ, C., Costello, M., Hollinger, A., Lennon, N. J., Hegarty, R., … Jaffe, D. B. (2013). Characterizing and measuring bias in sequence data. Genome Biology , 14 (5), R51. doi:10.1186/gb-2013-14-5-r51
Schultz, J. A., & Hebert, P. D. N. (2022). Do pseudogenes pose a problem for metabarcoding marine animal communities? Molecular Ecology Resources , n/a (n/a). doi:https://doi.org/10.1111/1755-0998.13667
Song, H., Buhay, J. E., Whiting, M. F., & Crandall, K. A. (2008). Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. Proceedings of the National Academy of Sciences , 105 (36), 13486–13491. doi:10.1073/pnas.0803076105
Sorenson, M. D., & Quinn, T. W. (1998). Numts: A challenge for avian systematics and population biology. The Auk , 115 (1), 214–221. doi:10.2307/4089130
Straub, S. C. K., Parks, M., Weitemier, K., Fishbein, M., Cronn, R. C., & Liston, A. (2012). Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics. American Journal of Botany , 99 (2), 349–64. doi:10.3732/ajb.1100335
The Darwin Tree of Life Project Consortium. (2022). Sequence locally, think globally: The Darwin Tree of Life Project. Proceedings of the National Academy of Sciences , 119 (4), e2115642118. doi:10.1073/pnas.2115642118
Twyford, A. D., & Ness, R. W. (2016). Strategies for complete plastid genome sequencing. Molecular Ecology Resources . doi:10.1111/1755-0998.12626
Vasimuddin, M., Misra, S., Li, H., & Aluru, S. (2019). Efficient Architecture-Aware Acceleration of BWA-MEM for Multicore Systems. In2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS) (pp. 314–324). doi:10.1109/IPDPS.2019.00041
Vaughan, H. E., Heslop-Harrison, J. S., & Hewitt, G. M. (1999). The localization of mitochondrial sequences to chromosomal DNA in orthopterans. Genome , 42 (5), 874–880. doi:10.1139/g99-020
Vendrami, D. L. J., Gossmann, T. I., Chakarov, N., Paijmans, A. J., Eyre-Walker, A., Forcada, J., & Hoffman, J. I. (2022). Signatures of selection on mitonuclear integrated genes uncover hidden mitogenomic variation in fur seals. Genome Biology and Evolution , evac104. doi:10.1093/gbe/evac104
Westerman, M., Barton, N. H., & Hewitt, G. M. (1987). Differences in DNA content between two chromosomal races of the grasshopperPodisma pedestris . Heredity , 58 (2), 221–228. doi:10.1038/hdy.1987.36
Wicke, S., Schneeweiss, G. M., DePamphilis, C. W., Müller, K. F., & Quandt, D. (2011). The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. Plant Molecular Biology , 76 (3–5), 273–97. doi:10.1007/s11103-011-9762-4
Woischnik, M., & Moraes, C. T. (2002). Pattern of organization of human mitochondrial pseudogenes in the nuclear genome. Genome Research ,12 (6), 885–893. doi:10.1101/gr.227202
Zhan, X., Pan, S., Wang, J., Dixon, A., He, J., Muller, M. G., … Bruford, M. W. (2013). Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle. Nature Genetics , 45 (5), 563–566. doi:10.1038/ng.2588
Zhang, D.-X., & Hewitt, G. M. (1996a). Highly conserved nuclear copies of the mitochondrial control region in the desert locustSchistocerca gregaria : some implications for population studies.Molecular Ecology , 5 (2), 295–300. doi:https://doi.org/10.1046/j.1365-294X.1996.00078.x
Zhang, D.-X., & Hewitt, G. M. (1996b). Nuclear integrations: challenges for mitochondrial DNA markers. Trends in Ecology & Evolution ,11 (6), 247–251. doi:10.1016/0169-5347(96)10031-8