Schwabl, 2021, Colonization and genetic diversification processes of Leishmania infantum in the Americas, Commun. Biol., 4, 139, 10.1038/s42003-021-01658-5
Lepers, 2021, Inference with selection, varying population size, and evolving population structure: application of ABC to a forward-backward coalescent process with interactions, Heredity, 126, 335, 10.1038/s41437-020-00381-x
Thogmartin, 2017, Monarch butterfly population decline in North America: identifying the threatening processes, R. Soc. Open Sci., 4, 170760, 10.1098/rsos.170760
Pleasants, 2017, Interpreting surveys to estimate the size of the monarch butterfly population: pitfalls and prospects, PLoS One, 12, 10.1371/journal.pone.0181245
Brower, 2012, Decline of monarch butterflies overwintering in Mexico: is the migratory phenomenon at risk?, Insect Conserv. Divers., 5, 95, 10.1111/j.1752-4598.2011.00142.x
Haan, 2019, The importance of shifting disturbance regimes in monarch butterfly decline and recovery, Front. Ecol. Evol., 7, 10.3389/fevo.2019.00191
Boyle, 2019, Monarch butterfly and milkweed declines substantially predate the use of genetically modified crops, Proc. Natl. Acad. Sci. USA, 116, 3006, 10.1073/pnas.1811437116
Inamine, 2016, Linking the continental migratory cycle of the monarch butterfly to understand its population decline, Oikos, 125, 1081, 10.1111/oik.03196
Zylstra, 2021, Changes in climate drive recent monarch butterfly dynamics, Nat. Ecol. Evol., 5, 1441, 10.1038/s41559-021-01504-1
Vane-Wright, 1993, The Columbus hypothesis: an explanation for the dramatic 19th century range expansion of the monarch butterfly
Brower, 1995, Understanding and misunderstanding the migration of the monarch butterfly (Nymphalidae) in North America: 1857–1995, J. Lepidopterists Soc.
Pudlo, 2016, Reliable ABC model choice via random forests, Bioinformatics, 32, 859, 10.1093/bioinformatics/btv684
Sisson, 2018, Overview of ABC, 3
Beaumont, 2002, Approximate Bayesian computation in population genetics, Genetics, 162, 2025, 10.1093/genetics/162.4.2025
Raynal, 2019, ABC random forests for Bayesian parameter inference, Bioinformatics Oxf. Engl., 35, 1720, 10.1093/bioinformatics/bty867
Lombaert, 2018, Colonization history of the western corn rootworm (Diabrotica virgifera virgifera) in North America: insights from random forest ABC using microsatellite data, Biol. Invasions, 20, 665, 10.1007/s10530-017-1566-2
Nevado, 2020, Rapid homoploid hybrid speciation in British gardens: the origin of Oxford Ragwort (Senecio Squalidus), Mol. Ecol., 29, 4221, 10.1111/mec.15630
Smith, 2018, Demographic inference in barn swallows using whole-genome data shows signal for bottleneck and subspecies differentiation during the Holocene, Mol. Ecol., 27, 4200, 10.1111/mec.14854
Estoup, 2018, Application of ABC to infer the genetic history of Pygmy hunter-gatherer populations from western central Africa
Boheemen, 2017, Multiple introductions, admixture and bridgehead invasion characterize the introduction history of Ambrosia artemisiifolia in Europe and Australia, Mol. Ecol., 26, 5421, 10.1111/mec.14293
Vallejo-Marín, 2021, Population genomic and historical analysis suggests a global invasion by bridgehead processes in Mimulus guttatus, Commun. Biol., 4, 327, 10.1038/s42003-021-01795-x
Fraimout, 2017, Deciphering the routes of invasion of drosophila Suzukii by means of ABC random forest, Mol. Biol. Evol., 34, 980
Clark, 2009, The last glacial maximum, Science, 325, 710, 10.1126/science.1172873
Pleasants, 2013, Milkweed loss in agricultural fields because of herbicide use: effect on the monarch butterfly population, Insect Conserv. Divers., 6, 135, 10.1111/j.1752-4598.2012.00196.x
Pleasants, 2017, Milkweed loss in agricultural fields because of herbicide use: effect on the monarch butterfly population, Insect Conserv. Divers., 6, 135, 10.1111/j.1752-4598.2012.00196.x
Weitemier, 2019, A draft genome and transcriptome of common milkweed (Asclepias syriaca) as resources for evolutionary, ecological, and molecular studies in milkweeds and Apocynaceae, PeerJ, 7, 10.7717/peerj.7649
Zhan, 2014, The genetics of monarch butterfly migration and warning colouration, Nature, 514, 317, 10.1038/nature13812
2021
Evanno, 2005, Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study, Mol. Ecol., 14, 2611, 10.1111/j.1365-294X.2005.02553.x
Talla, 2020, Genomic evidence for gene flow between monarchs with divergent migratory phenotypes and flight performance, Mol. Ecol., 29, 2567, 10.1111/mec.15508
Janes, 2017, The K = 2 conundrum, Mol. Ecol., 26, 3594, 10.1111/mec.14187
Hemstrom, 2022, Population genetics of a recent range expansion and subsequent loss of migration in monarch butterflies, Mol. Ecol., 31, 4544, 10.1111/mec.16592
Lyons, 2012, Lack of genetic differentiation between monarch butterflies with divergent migration destinations, Mol. Ecol., 21, 3433, 10.1111/j.1365-294X.2012.05613.x
Csilléry, 2012, Abc: an R package for approximate Bayesian computation (ABC), Methods Ecol. Evol., 3, 475, 10.1111/j.2041-210X.2011.00179.x
Semmens, 2016, Quasi-extinction risk and population targets for the Eastern, migratory population of monarch butterflies (Danaus plexippus), Sci. Rep., 6, 23265, 10.1038/srep23265
Marçais, 2011, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers, Bioinformatics, 27, 764, 10.1093/bioinformatics/btr011
Vurture, 2017, GenomeScope: fast reference-free genome profiling from short reads, Bioinformatics, 33, 2202, 10.1093/bioinformatics/btx153
Chin, 2016, Phased diploid genome assembly with single-molecule real-time sequencing, Nat. Methods, 13, 1050, 10.1038/nmeth.4035
Roach, 2018, Purge haplotigs: allelic contig reassignment for third-gen diploid genome assemblies, BMC Bioinformatics, 19, 460, 10.1186/s12859-018-2485-7
Dudchenko, 2017, De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds, Science, 356, 92, 10.1126/science.aal3327
Xu, 2019, LR_Gapcloser: a tiling path-based gap closer that uses long reads to complete genome assembly, GigaScience, 8, 10.1093/gigascience/giy157
Ou, 2018, LTR_retriever: a highly accurate and sensitive program for identification of long terminal repeat retrotransposons, Plant Physiol., 176, 1410, 10.1104/pp.17.01310
Ellinghaus, 2008, LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons, BMC Bioinformatics, 9, 18, 10.1186/1471-2105-9-18
Xu, 2007, LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons, Nucleic Acids Res., 35, 10.1093/nar/gkm286
Smit, 2013
Altschul, 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403, 10.1016/S0022-2836(05)80360-2
Campbell, 2014, MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations, Plant Physiol., 164, 513, 10.1104/pp.113.230144
Kim, 2015, HISAT: a fast spliced aligner with low memory requirements, Nat. Methods, 12, 357, 10.1038/nmeth.3317
Mapleson, 2018, Efficient and accurate detection of splice junctions from RNA-seq with portcullis, GigaScience, 7, 10.1093/gigascience/giy131
Venturini, 2018, Leveraging multiple transcriptome assembly methods for improved gene structure annotation, GigaScience, 7, 10.1093/gigascience/giy093
Stanke, 2008, Using native and syntenically mapped CDNA alignments to improve de novo gene finding, Bioinformatics, 24, 637, 10.1093/bioinformatics/btn013
Korf, 2004, Gene finding in novel genomes, BMC Bioinformatics, 5, 59, 10.1186/1471-2105-5-59
Cantarel, 2008, MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes, Genome Res., 18, 188, 10.1101/gr.6743907
Boutet, 2007, UniProtKB/Swiss-Prot, 89
Jones, 2014, InterProScan 5: genome-scale protein function classification, Bioinformatics, 30, 1236, 10.1093/bioinformatics/btu031
Waterhouse, 2018, BUSCO applications from quality assessments to gene prediction and phylogenomics, Mol. Biol. Evol., 35, 543, 10.1093/molbev/msx319
Fulton, 1995, Microprep protocol for extraction of DNA from tomato and other herbaceous plants, Plant Mol. Biol. Rep., 13, 207, 10.1007/BF02670897
Elshire, 2011, A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species, PLoS One, 6, 10.1371/journal.pone.0019379
Rochette, 2019, Stacks 2: analytical methods for paired-end sequencing improve RADseq-based population genomics, Mol. Ecol., 28, 4737, 10.1111/mec.15253
Catchen, 2013, Stacks: an analysis tool set for population genomics, Mol. Ecol., 22, 3124, 10.1111/mec.12354
Langmead, 2012, Fast gapped-read alignment with bowtie 2, Nat. Methods, 9, 357, 10.1038/nmeth.1923
Li, 2009, The sequence alignment/map format and SAMtools, Bioinformatics Oxf. Engl., 25, 2078, 10.1093/bioinformatics/btp352
Jombart, 2008, Adegenet: a R package for the multivariate analysis of genetic markers, Bioinformatics Oxf. Engl., 24, 1403, 10.1093/bioinformatics/btn129
Jombart, 2011, Adegenet 1.3-1: new tools for the analysis of genome-wide SNP data, Bioinformatics Oxf. Engl., 27, 3070, 10.1093/bioinformatics/btr521
Danecek, 2011, The variant call format and VCFtools, Bioinformatics, 27, 2156, 10.1093/bioinformatics/btr330
2015
McKenna, 2010, The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res., 20, 1297, 10.1101/gr.107524.110
DePristo, 2011, A framework for variation discovery and genotyping using next-generation DNA sequencing data, Nat. Genet., 43, 491, 10.1038/ng.806
Van der Auwera, 2013, From FastQ data to high confidence variant calls: the genome analysis toolkit best practices pipeline, Curr Protoc Bioinformatics, 43, 11.10.1, 10.1002/0471250953.bi1110s43
Zhan, 2011, The monarch butterfly genome yields insights into long-distance migration, Cell, 147, 1171, 10.1016/j.cell.2011.09.052
Goudet, 2005, Hierfstat, a package for r to compute and test hierarchical F-statistics, Mol. Ecol. Notes, 5, 184, 10.1111/j.1471-8286.2004.00828.x
Paradis, 2010, Pegas: an R package for population genetics with an integrated-modular approach, Bioinformatics Oxf. Engl., 26, 419, 10.1093/bioinformatics/btp696
Kamvar, 2014, Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction, PeerJ, 2, 10.7717/peerj.281
Pritchard, 2000, Inference of population structure using multilocus genotype data, Genetics, 155, 945, 10.1093/genetics/155.2.945
Earl, 2012, STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method, Conserv. Genet. Resour., 4, 359, 10.1007/s12686-011-9548-7
Jakobsson, 2007, CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure, Bioinformatics Oxf. Engl., 23, 1801, 10.1093/bioinformatics/btm233
Dray, 2007, The ade4 package: implementing the duality diagram for ecologists, J. Stat. Software, 22, 1
Chessel, 2004, The ade4 package-I: one-table methods, R News, 4, 5
Cornuet, 2014, DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data, Bioinformatics Oxf. Engl., 30, 1187, 10.1093/bioinformatics/btt763
Bhowmik, P.C., and Bandeen, J.D.. The biology of Canadian weeds: 19. Asclepias syriaca L. Can. J. Plant Sci. 56, 579–589.