Temporal matches between monarch butterfly and milkweed population changes over the past 25,000 years
Tài liệu tham khảo
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.