References
- Abbott R., Albach D., Ansell S., Arntzen J.W., Baird S.J.E., Bierne N., Boughman J., Brelsford A., Buerkle C.A., Buggs R., Butlin R.K., Dieckmann U., Eroukhmanoff F., Grill A., Cahan S.H., Hermansen J.S., Hewitt G., Hudson A.G., Jiggins C., Jones J., Keller B., Marczewski T., Mallet J., Martinez-Rodriguez P., Möst M., Mullen S., Nichols R., Nolte A.W., Parisod C., Pfennig K., Rice A.M., Ritchie M.G., Seifert B., Smadja C.M., Stelkens R., Szymura J.M., Väinölä R., Wolf J.B.W., Zinner D. (2013). Hybridization and speciation. J. Evol. Biol., 26: 229–246.10.1111/j.1420-9101.2012.02599.x
- Adavoudi R., Pilot M. (2022). Consequences of hybridization in mammals: A systematic review. Genes, 13: 50.10.3390/genes13010050
- Allen R., Ryan H., Davis B.W., King C., Frantz L., Irving-Pease E., Barnett R., Linderholm A., Loog L., Haile J., Lebrasseur O., White M., Kitchener A.C., Murphy W.J., Larson G. (2020). A mitochondrial genetic divergence proxy predicts the reproductive compatibility of mammalian hybrids. Proc. R. Soc. B Biol. Sci., 287: 20200690.10.1098/rspb.2020.0690
- Barreta J., Gutiérrez-Gil B., Iñiguez V., Saavedra V., Chiri R., Latorre E., Arranz J.J. (2013). Analysis of mitochondrial DNA in Bolivian llama, alpaca and vicuna populations: A contribution to the phylogeny of the South American camelids. Anim. Genet., 44: 158–168.10.1111/j.1365-2052.2012.02376.x
- Behjati S., Tarpey P.S. (2013). What is next generation sequencing? Arch. Dis. Child. Educ. Pract. Ed., 98: 236–238.10.1136/archdischild-2013-304340
- Beissinger T.M., Hirsch C.N., Sekhon R.S., Foerster J.M., Johnson J.M., Muttoni G., Vaillancourt B., Robin Buell C., Kaeppler S.M., de Leon N. (2013). Marker density and read depth for genotyping populations using genotyping-by-sequencing. Genetics, 193: 1073–1081.10.1534/genetics.112.147710
- Berbel-Filho W.M., Tatarenkov A., Pacheco G., Espírito-Santo H.M.V., Lira M.G., de Leaniz C.G., Avise J.C., Lima S.M.Q., Rodríguez-López C.M., Consuegra S. (2021). Against the odds: Hybrid zones between mangrove killifish species with different mating systems. Genes, 12: 1486.10.3390/genes12101486
- Calderon M., More M.J., Gutierrez G.A., Abel Ponce de León F. (2021). Development of a 76K alpaca (Vicugna pacos) single nucleotide polymorphisms (SNPs) microarray. Genes, 12: 1–18.10.3390/genes12020291
- Cordeiro E.M.G., Pantoja-Gomez L.M., De Paiva J.B., Nascimento A.R.B., Omoto C., Michel A.P., Correa A.S. (2020). Hybridization and introgression between Helicoverpa armigera and H. zea: An adaptational bridge. BMC Evol. Biol., 20: 1–12.10.1186/s12862-020-01621-8
- Davey J.W., Hohenlohe P.A., Etter P.D., Boone J.Q., Catchen J.M., Blaxter M.L. (2011). Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat. Rev. Genet., 12: 499–510.10.1038/nrg3012
- De Donato M., Peters S.O., Mitchell S.E., Hussain T., Imumorin I.G. (2013). Genotyping-by-Sequencing (GBS): A novel, efficient and cost-effective genotyping method for cattle using next-generation sequencing. PLoS ONE, 8: 62137.10.1371/journal.pone.0062137
- Deschamps S., Llaca V., May G.D. (2012). Genotyping-by-sequencing in plants. Biology, 1: 460–483.10.3390/biology1030460
- Díaz-Maroto P., Rey-Iglesia A., Cartajena I., Núñez L., Westbury M.V., Varas V., Moraga M., Campos P.F., Orozco-terWenge P., Marín J.C., Hansen A.J. (2021). Ancient DNA reveals the lost domestication history of south american camelids in Northern Chile and across the andes. eLife, 10: e63390.10.7554/eLife.63390
- Di Rocco F., Posik D.M., Ripoli M.V., Díaz S., Maté M.L., Giovambattista G., Vidal-Rioja L. (2011). South American camelid illegal traffic detection by means of molecular markers. Leg. Med., 13: 289–292.10.1016/j.legalmed.2011.08.001
- Dupuis J.R., Brunet B.M.T., Bird H.M., Lumley L.M., Fagua G., Boyle B., Levesque R., Cusson M., Powell J.A., Sperling F.A.H. (2017). Genome-wide SNPs resolve phylogenetic relationships in the North American spruce budworm (Choristoneura fumiferana) species complex. Mol. Phylogenet. Evol., 111: 158–168.10.1016/j.ympev.2017.04.001
- Dupuis J.R., Sperling F.A.H. (2020). Phylogenomic test of mitochondrial clues to archaic ancestors in a group of hybridizing swallowtail butterflies. Mol. Phylogenet. Evol., 152: 106921.10.1016/j.ympev.2020.106921
- Echalar J., Barreta J. (2022). Introgression in domestic camelid productive systems in Bolivia. Small Rumin. Res., 214: 106742.10.1016/j.smallrumres.2022.106742
- Echalar J., Barreta J., Iniguez V., Romero F., Callisaya A.M., Saavedra V. (2020). Intraspecific genetic analysis of Bolivian alpacas and interspecific relationship with llamas and vicunas. Small Rumin. Res., 189: 106137.10.1016/j.smallrumres.2020.106137
- Ellegren H. (2014). Genome sequencing and population genomics in non-model organisms. Trends Ecol. Evol., 29: 51–63.10.1016/j.tree.2013.09.008
- Elshire R.J., Glaubitz J.C., Sun Q., Poland J.A., Kawamoto K., Buckler E.S., Mitchell S.E. (2011). A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE, 6: e19379.10.1371/journal.pone.0019379
- Fan R., Gu Z., Guang X., Marín J.C., Varas V., González B.A., Wheeler J.C., Hu Y., Li E., Sun X., Yang X., Zhang C., Gao W., He J., Munch K., Corbett-Detig R., Barbato M., Pan S., Zhan X., Bruford M.W., Dong C. (2020). Genomic analysis of the domestication and post-Spanish conquest evolution of the llama and alpaca. Genome Biol., 21: 1–26.10.1186/s13059-020-02080-6
- Forsdick N.J., Martini D., Brown L., Cross H.B., Maloney R.F., Steeves T.E., Knapp M. (2021). Genomic sequencing confirms absence of introgression despite past hybridisation between a critically endangered bird and its common congener. Glob. Ecol. Conserv., 28: e01681.10.1016/j.gecco.2021.e01681
- Gabryś J., Kij B., Kochan J., Bugno-Poniewierska M. (2021). Interspecific hybrids of animals in nature, breeding and science – a review. Ann. Anim. Sci., 21: 403–415.10.2478/aoas-2020-0082
- Germain E., Benhamou S., Poulle M.L. (2008). Spatio-temporal sharing between the European wildcat, the domestic cat and their hybrids. J. Zool., 276: 195–203.10.1111/j.1469-7998.2008.00479.x
- Graham C.F., Eberts R.L., Goncin U., Somers C.M. (2021). Spontaneous hybridization and introgression between walleye (Sander vitreus) and sauger (Sander canadensis) in two large reservoirs: Insights from genotyping by sequencing. Evol. Appl., 14: 965–982.10.1111/eva.13174
- Gurgul A., Miksza-Cybulska A., Szmatoła T., Jasielczuk I., Piestrzyńska-Kajtoch A., Fornal A., Semik-Gurgul E., Bugno-Poniewierska M. (2019 a). Genotyping-by-sequencing performance in selected livestock species. Genomics, 111: 186–195.10.1016/j.ygeno.2018.02.00229427639
- Gurgul A., Miksza-Cybulska A., Szmatoła T., Semik-Gurgul E., Jasielczuk I., Bugno-Poniewierska M., Figarski T., Kajtoch Ł. (2019 b). Evaluation of genotyping by sequencing for population genetics of sibling and hybridizing birds: an example using Syrian and Great Spotted Woodpeckers. J. Ornithol., 160: 287–294.10.1007/s10336-018-1601-9
- Kadwell M., Fernandez M., Stanley H.F., Baldi R., Wheeler J.C., Rosadio R., Bruford M.W. (2001). Genetic analysis reveals the wild ancestors of the llama and the alpaca. Proc. R. Soc. B Biol. Sci., 268: 2575–2584.10.1098/rspb.2001.1774
- Kim C., Guo H., Kong W., Chandnani R., Shuang L.S., Paterson A.H. (2016). Application of genotyping by sequencing technology to a variety of crop breeding programs. Plant Sci., 242: 14–22.10.1016/j.plantsci.2015.04.016
- Marín J.C., Romero K., Rivera R., Johnson W.E., González B.A. (2017). Y-chromosome and mtDNA variation confirms independent domestications and directional hybridization in South American camelids. Anim. Genet., 48: 591–595.10.1111/age.12570
- Marques D.A., Meier J.I., Seehausen O. (2019). A combinatorial view on speciation and adaptive radiation. Trends Ecol. Evol., 34: 531–544.10.1016/j.tree.2019.02.008
- Maté M.L., Di Rocco F., Zambelli A., Vidal-Rioja L. (2007). Mitochondrial heteroplasmy in Control Region DNA of South American camelids. Small Rumin. Res., 71: 123–129.10.1016/j.smallrumres.2006.04.016
- Maté M.L., Di Rocco F., Zambelli A., Vidal-Rioja L. (2004). Mitochondrial DNA structure and organization of the control region of South American camelids. Mol. Ecol. Notes, 4: 765–767.10.1111/j.1471-8286.2004.00744.x
- McFarlane S.E., Pemberton J.M. (2019). Detecting the true extent of introgression during anthropogenic hybridization. Trends Ecol. Evol., 34: 315–326.10.1016/j.tree.2018.12.013
- Melo C., Manunza A., Melo M., Olivera L., Amills M. (2012). Analysis of the mitochondrial diversity of alpacas in eight farming areas of the south of Peru, in: Fibre Production in South American Camelids and Other Fibre Animals. Wageningen Academic Publishers, pp. 87–91.10.3920/978-90-8686-727-1_10
- More M., Gutiérrez G., Rothschild M., Bertolini F., Abel Ponce De León F. (2019). Evaluation of SNP genotyping in alpacas using the bovine HD genotyping beadchip. Front. Genet., 10: 361.10.3389/fgene.2019.00361
- Myers E.A. (2021). Genome-wide data reveal extensive gene flow during the diversification of the western rattlesnakes (Viperidae: Crotalinae: Crotalus). Mol. Phylogenet. Evol., 165: 107313.10.1016/j.ympev.2021.107313
- Narum S.R., Buerkle C.A., Davey J.W., Miller M.R., Hohenlohe P.A. (2013). Genotyping-by-sequencing in ecological and conservation genomics. Mol. Ecol., 22: 2841–2847.10.1111/mec.12350
- Pacheco-Sierra G., Vázquez-Domínguez E., Pérez-Alquicira J., Suárez-Atilano M., Domínguez-Laso J. (2018). Ancestral hybridization yields evolutionary distinct hybrids lineages and species boundaries in crocodiles, posing unique conservation conundrums. Front. Ecol. Evol., 6: 138.10.3389/fevo.2018.00138
- Pazmiño D.A., van Herderden L., Simpfendorfer C.A., Junge C., Donnellan S.C., Hoyos-Padilla E.M., Duffy C.A.J., Huveneers C., Gillanders B.M., Butcher P.A., Maes G.E. (2019). Introgressive hybridisation between two widespread sharks in the east Pacific region. Mol. Phylogenet. Evol., 136: 119–127.10.1016/j.ympev.2019.04.013
- Pfennig K.S. (2021). Biased hybridization and its impact on adaptive introgression. Trends Ecol. Evol., 36: 488–497.10.1016/j.tree.2021.02.010
- Podbielska A., Piórkowska K. (2022). Examination of D-loop region and DBY gene as tools for identifying hybridisation in alpacas (Vicugna pacos) based on Polish populations. Small Rumin. Res., 211: 106690.10.1016/j.smallrumres.2022.106690
- Podbielska A., Piórkowska K., Szmatoła T. (2021). Microsatellite-based genetic structure and hybrid detection in alpacas bred in poland. Animals, 11: 2193.10.3390/ani11082193
- Poland J., Endelman J., Dawson J., Rutkoski J., Wu S., Manes Y., Dreisigacker S., Crossa J., Sánchez-Villeda H., Sorrells M., Jannink J.-L. (2012). Genomic selection in wheat breeding using genotyping-by-sequencing. Plant Genome, 5.10.3835/plantgenome2012.06.0006
- Poland J.A., Rife T.W. (2012). Genotyping-by-sequencing for plant breeding and genetics. Plant Genome, 5.10.3835/plantgenome2012.05.0005
- Ramírez-Reyes T., Blair C., Flores-Villela O., Piñero D., Lathrop A., Murphy R. (2020). Phylogenomics and molecular species delimitation reveals great cryptic diversity of leaf-toed geckos (Phyllodactylidae: Phyllodactylus), ancient origins, and diversification in Mexico. Mol. Phylogenet.Evol., 150: 106880.10.1016/j.ympev.2020.106880
- Richardson M.F., Munyard K., Croft L.J., Allnutt T.R., Jackling F., Alshanbari F., Jevit M., Wright G.A., Cransberg R., Tibary A., Perelman P., Appleton B., Raudsepp T. (2019). Chromosome-level alpaca reference genome VicPac3.1 improves genomic insight into the biology of new world camelids. Front. Genet., 10: 586.10.3389/fgene.2019.00586
- Seneviratne S.S., Davidson P., Martin K., Irwin D.E. (2016). Low levels of hybridization across two contact zones among three species of woodpeckers (Sphyrapicus sapsuckers). J. Avian Biol., 47: 887–898.10.1111/jav.00946
- Sonah H., Bastien M., Iquira E., Tardivel A., Légaré G., Boyle B., Normandeau É., Laroche J., Larose S., Jean M., Belzile F. (2013). An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PLoS ONE, 8: e54603.10.1371/journal.pone.0054603
- Stanley H.F., Kadwell M., Wheeler J.C. (1994). Molecular evolution of the family Camelidae: A mitochondrial DNA study. Proc. R. Soc. B Biol. Sci., 256: 1–6.10.1098/rspb.1994.0041
- Thermes C. (2014). Ten years of next-generation sequencing technology. Trends Genet., 30: 418–426.10.1016/j.tig.2014.07.001
- Torkamaneh D., Laroche J., Belzile F. (2016). Genome-wide SNP calling from genotyping by sequencing (GBS) data: A comparison of seven pipelines and two sequencing technologies. PLoS ONE, 11: 0161333.10.1371/journal.pone.0161333
- Varas V., Vásquez J.P., Rivera R., Longo A., Valdecantos P.A., Wheeler J.C., Johnson W.E., Marín J.C. (2020). Interbreeding among South American camelids threatens species integrity. J. Arid Environ., 181: 104249.10.1016/j.jaridenv.2020.104249
- Wheeler J.C. (1995 a). Evolution and present situation of the South American camelidae. Biol. J. Linn. Soc., 54: 271–295.10.1016/0024-4066(95)90021-7
- Wheeler J.C., Russel A.J.F., Redden H. (1995 b). Llamas and Alpacas: Pre-conquest breeds and post-conquest hybrids. J. Archaeol. Sci., 22: 833–840.10.1016/0305-4403(95)90012-8
- Wheeler J.C. (2012). South American camelids – past, present and future. J. Camelid Sci., 5: 1–24.
- Yadav A.D., Sahu J.D., Dubey A.D., Gadpayle R.D., Kiran Barwa D., Kashyap K., Yadav A., Jain A., Sahu J., Dubey A., Gadpayle R., Kiran Barwa D., Verma U. (2019). An overview on species hybridization in animals. Int. J. Fauna Biol. Stud., 6: 36–42.
- Yue G.H., Wang L. (2017). Current status of genome sequencing and its applications in aquaculture. Aquaculture, 468: 337–347.10.1016/j.aquaculture.2016.10.036