Bibliography
Altschul, S. F., W. Gish, W. Miller, E. W. Myers and D. J. Lipman, 1990
Basic local alignment search tool. Journal of Molecular Biology
215: 403-410.
Antunes, J. T., P. N. Leao and V. M. Vasconcelos, 2015Cylindrospermopsis raciborskii: review of the distribution,
phylogeography, and ecophysiology of a global invasive species.
Frontiers in Microbiology 6: 473.
Arechederra-Romero, L., 2012 Southwest Fire Science Consortium Field
Trip to the Chiricahua National Monument: Discussion of the Impacts of
the 2011 Horseshoe 2 Fire, pp. in Arizona Geology Magazine ,
Arizona Geology Magazine.
Astanei, I., E. Gosling, J. Wilson and E. Powell, 2005 Genetic
variability and phylogeography of the invasive zebra mussel,Dreissena polymorpha (Pallas) . Mol Ecol 14: 1655-1666.
Avgar, T., G. Street, and J. M. Fryxell, 2014 On the adaptive benefits
of mammal migration. Canadian Journal of Zoology 92: 481-490.
Bao, W., K. K. Kojima and O. Kohany, 2015 Repbase Update, a database of
repetitive elements in eukaryotic genomes. Mobile DNA 6: 4-9.
Behrman, E. L., S. S. Watson, K. R. O’Brien, S. M. Heschel and P. S.
Schmidt, 2015 Seasonal variation in life history traits in twoDrosophila species. Journal of Evolutionary Biology 28:1691-1704.
Buffalo, V., 2018 Scythe .
Burt, A., and R. Trivers, 2006 Genes in Conflict.
Chakraborty, M., R. Zhao, X. Zhang, S. Kalsow and J. J. Emerson, 2017
Extensive hidden genetic variation shapes the structure of functional
elements in Drosophila . Doi.Org 50: 114967.
Chapman, J. R., T. Hill and R. L. Unckless, 2019 Balancing selection
drives maintenance of genetic variation in Drosophilaantimicrobial peptides. Genome Biology and Evolution 11:2691-2701.
Charlesworth, B., D. Charlesworth and N. H. Barton, 2003 The Effects of
Genetic and Geographic Structure on Neutral Variation. Annual Review of
Ecology, Evolution, and Systematics 34: 99-125.
Charlesworth, B., and C. H. Langley, 1989 The population genetics ofDrosophila transposable elements. Annual review of genetics
23: 251-287.
Charlesworth, B., C. H. Langley and P. D. Sniegowski, 1997 Transposable
element distributions in Drosophila . Genetics 147:1993-1995.
Chen, X., O. Schulz-Trieglaff, R. Shaw, B. Barnes, F. Schlesingeret al. , 2016 Manta: Rapid detection of structural variants and
indels for germline and cancer sequencing applications. Bioinformatics
32: 1220-1222.
Cingolani, P., A. Platts, L. L. Wang, M. Coon, T. Nguyen et al. ,
2012 A program for annotating and predicting the effects of single
nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila
melanogaster strain w1118; iso-2; iso-3. Fly 6: 80-92.
Cini, A., C. Ioriatti and G. Anfora, 2012 A review of the invasion ofDrosophila suzukii in Europe and a draft research agenda for
integrated pest management. Bulletin of Insectology 65:149-160.
Cloudsley-Thompson, J. L., 1978 Human Activities and Desert Expansion.
The Geographical Journal 144: 416-423.
Coe, S. J., D. M. Finch and M. M. Friggens, 2012 An Assessment of
Climate Change and the Vulnerability of Wildlife in the Sky Islands of
the Southwest, pp. 1-208. United States Department of Agriculture.
Cruickshank, T. E., and M. W. Hahn, 2014 Reanalysis suggests that
genomic islands of speciation are due to reduced diversity, not reduced
gene flow. Mol Ecol 23: 3133-3157.
Cutter, A. D., and B. A. Payseur, 2013 Genomic signatures of selection
at linked sites: unifying the disparity among species. Nat Rev Genet
14: 262-274.
Danecek, P., A. Auton, G. Abecasis, C. A. Albers, E. Banks et
al. , 2011 The variant call format and VCFtools. Bioinformatics
27: 2156-2158.
DePristo, M. A., E. Banks, R. Poplin, K. V. Garimella, J. R. Maguireet al. , 2011 A framework for variation discovery and genotyping
using next-generation DNA sequencing data. Nature genetics 43:491-498.
Dobzhansky, T., and B. Spassky, 1968 The Genetics of Natural Populations
XL: Heterotic and Deleterious Effects of Recessive Lethals in
Populations of Drosophila pseudoobscura . Genetics 59:411-425.
Dobzhansky, T., and A. H. Sturtevant, 1937 Inversions In Chromosomes ofDrosophila pseudoobscura. Genetics 23: 28-64.
Dobzhansky, T. H., A. S. Hunter, O. Pavlovsky, B. Spassky and B.
Wallace, 1963 Genetics of natural populations. XXXI. Genetics of an
isolated marginal population of Drosophila pseudoobscura .
Genetics 48: 91-103.
Dostert, C., E. Jouanguy, P. Irving, L. Troxler, D. Galiana-Arnouxet al. , 2005 The Jak-STAT signaling pathway is required but not
sufficient for the antiviral response of Drosophila. Nat Immunol
6: 946-953.
Dyer, K. A., 2004 Evolutionarily Stable Infection by a Male-Killing
Endosymbiont in Drosophila innubila : Molecular Evidence From the
Host and Parasite Genomes. Genetics 168: 1443-1455.
Dyer, K. a., and J. Jaenike, 2005 Evolutionary dynamics of a spatially
structured host-parasite association: Drosophila innubila and
male-killing Wolbachia . Evolution; international journal of
organic evolution 59: 1518-1528.
Dyer, K. A., M. S. Minhas and J. Jaenike, 2005 Expression and modulation
of embryonic male-killing in Drosophila innubila : opportunities
for multilevel selection. Evolution; international journal of organic
evolution 59: 838-848.
Eilertson, K. E., J. G. Booth and C. D. Bustamante, 2012 SnIPRE:
Selection Inference Using a Poisson Random Effects Model. PLoS
Computational Biology 8.
Excoffier, L., M. Foll and R. J. Petit, 2009 Genetic Consequences of
Range Expansions. Annual Review of Ecology, Evolution, and Systematics
40: 481-501.
Falush, D., M. Stephens and J. K. Pritchard, 2003 Inference of
population structure using multilocus genotype data: Linked loci and
correlated allele frequencies. Genetics 164: 1567-1587.
Frichot, E., F. Mathieu, T. Trouillon, G. Bouchard and O. François, 2014
Fast and efficient estimation of individual ancestry coefficients.
Genetics 196: 973-983.
Fuller, Z. L., G. D. Haynes, S. Richards and S. W. Schaeffer, 2016
Genomics of Natural Populations: How Differentially Expressed Genes
Shape the Evolution of Chromosomal Inversions in. Genetics.
Gao, Z., D. Waggoner, M. Stephens, C. Ober and M. Przeworski, 2015 An
estimate of the average number of recessive lethal mutations carried by
humans. Genetics 199: 1243-1254.
Garrido-Ramos, M. A., 2017 Satellite DNA: An Evolving Topic. Genes
(Basel) 8.
Gillespie, J., 2004 Population Genetics: A Concise Guide. 232.
Goubert, C., L. Modolo, C. Vieira, C. V. Moro, P. Mavingui et
al. , 2015 De novo assembly and annotation of the Asian tiger mosquito
(Aedes albopictus ) repeatome with dnaPipeTE from raw genomic
reads and comparative analysis with the yellow fever mosquito
(Aedes aegypti ). Genome Biology and Evolution 7:1192-1205.
Gramates, L. S., S. J. Marygold, G. Dos Santos, J. M. Urbano, G.
Antonazzo et al. , 2017 FlyBase at 25: Looking to the future.
Nucleic Acids Research 45: D663-D671.
Guindon, S., J.-F. Dufayard, V. Lefort, M. Anisimova, W. Hordijket al. , 2010 New algorithms and methods to estimate
maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.
Systematic biology 59: 307-321.
Haller, B. C., and P. W. Messer, 2017 asymptoticMK: A Web-Based Tool for
the Asymptotic McDonald–Kreitman Test. G3: Genes, Genomes, Genetics
7: 1569-1575.
Hermisson, J., and P. S. Pennings, 2005 Soft sweeps: molecular
population genetics of adaptation from standing genetic variation.
Genetics 169: 2335-2352.
Hewitt, G., 2000 The genetic legacy of the Quaternary ice ages. Nature
405: 907-913.
Hill, T., B. Koseva and R. L. Unckless, 2019 The genome ofDrosophila innubila reveals lineage-specific patterns of
selection in immune genes. Molecular Biology and Evolution:1-36.
Hill, T., and R. Unckless, 2020 Recurrent evolution of two competing
haplotypes in an insect DNA virus. Biorxiv: 1-45.
Hoban, S., J. L. Kelley, K. E. Lotterhos, M. F. Antolin, G. Bradburdet al. , 2016 Finding the Genomic Basis of Local Adaptation:
Pitfalls, Practical Solutions, and Future Directions. Am Nat
188: 379-397.
Hoffmann, J. A., 2003 The immune response of Drosophila . Nature
426: 33-38.
Holmgren, K., J. A. Lee-Thorp, G. R. J. Cooper, K. Lundblad, T. C.
Partridge et al. , 2003 Persistent millennial-scale climatic
variability over the past 25,000 years in Southern Africa. Quaternary
Science Reviews 22: 2311-2326.
Http://broadinstitute.github.io/picard, Picard .
Huber, C. D., M. DeGiorgio, I. Hellmann and R. Nielsen, 2016 Detecting
recent selective sweeps while controlling for mutation rate and
background selection. Mol Ecol 25: 142-156.
Imler, J., and I. Elftherianos, 2009 Drosophila as a model for
studying antiviral defences. Insect infection and immunity (eds Rolff
J., Reyolds SE): 49-68.
Jaenike, J., and K. A. Dyer, 2008 No resistance to male-killingWolbachia after thousands of years of infection. Journal of
Evolutionary Biology 21: 1570-1577.
Joshi, N., and J. Fass, 2011 Sickle: A sliding window, adaptive,
quality-based trimming tool for fastQ files. 1.33.
Kageyama, D., H. Anbutsu, M. Shimada and T. Fukatsu, 2009 Effects of
host genotype against the expression of spiroplasma-induced male killing
in Drosophila melanogaster. Heredity (Edinb) 102: 475-482.
Kofler, R., A. J. Betancourt and C. Schlötterer, 2012 Sequencing of
pooled DNA Samples ( Pool-Seq ) uncovers complex dynamics of
transposable element insertions in Drosophila melanogaster . PloS
Genetics 8: 1-16.
Kofler, R., G. Daniel and C. Schlötterer, 2016 PoPoolationTE2 :
comparative population genomics of transposable elements using Pool-Seq.
Molecular Biology and Evolution: 1-12.
Kofler, R., V. Nolte and C. Schlötterer, 2015 Tempo and mode of
transposable element activity in Drosophila . PLoS Genet
11: e1005406.
Korneliussen, T. S., A. Albrechtsen and R. Nielsen, 2014 ANGSD: Analysis
of Next Generation Sequencing Data. BMC Bioinformatics 15: 356.
Lachaise, D., and J.-F. Silvain, 2004 How two Afrotropical endemics made
two cosmopolitan human commensals: the Drosophila
melanogaster -D. simulans palaeogeographic riddle. Genetica
120: 17-39.
Lack, J. B., C. M. Cardeno, M. W. Crepeau, W. Taylor, R. B.
Corbett-Detig et al. , 2015 The Drosophila genome nexus: A
population genomic resource of 623 Drosophila melanogastergenomes, including 197 from a single ancestral range population.
Genetics 199: 1229-1241.
Li, H., and R. Durbin, 2009 Fast and accurate short read alignment with
Burrows-Wheeler transform. Bioinformatics (Oxford, England) 25:1754-1760.
Li, H., and R. Durbin, 2011 Inference of human population history from
individual whole-genome sequences. Nature 475: 493-496.
Li, H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al. ,
2009 The sequence alignment/map format and SAMtools. Bioinformatics
(Oxford, England) 25: 2078-2079.
Liu, X., and Y.-X. Fu, 2015 Exploring population size changes using SNP
frequency spectra. Nature genetics 47: 555-559.
Lower, S. S., M. P. McGurk, A. G. Clark and D. A. Barbash, 2018
Satellite DNA evolution: old ideas, new approaches. Curr Opin Genet Dev
49: 70-78.
Ma, X., J. L. Kelley, K. Eilertson, S. Musharoff, J. D. Degenhardtet al. , 2013 Population Genomic Analysis Reveals a Rich
Speciation and Demographic History of Orangutans (Pongo pygmaeusand Pongo abelii ). PLoS ONE 8.
Machado, C. a., T. S. Haselkorn and M. a. F. Noor, 2007 Evaluation of
the genomic extent of effects of fixed inversion differences on
intraspecific variation and interspecific gene flow in Drosophila
pseudoobscura and Drosophila persimilis . Genetics 175:1289-1306.
Machado, H. E., A. O. Bergland, K. R. O’Brien, E. L. Behrman, P. S.
Schmidt et al. , 2015 Comparative population genomics of
latitudinal variation in D. simulans and D. melanogaster .
Molecular Ecology: n/a-n/a.
Mackay, T. F. C., S. Richards, E. a. Stone, A. Barbadilla, J. F. Ayroleset al. , 2012 The Drosophila melanogaster genetic reference
panel. Nature 482: 173-178.
Marinkovic, D., 1967 Genetic Loads Affecting Fecundity in Natural
Populations of Drosophila pseudoobscura . Genetics:61-71.
Markow, T. A., and P. O’Grady, 2006 Drosophila : a guide to
species identification.
Martin, M., 2011 Cutadapt removes adapter sequences from high-throughput
sequencing reads. Technical Notes: 1-12.
Marzo, M., M. Puig and A. Ruiz, 2008 The Foldback-like element Galileo
belongs to the P superfamily of DNA transposons and is widespread within
the Drosophila genus. Proceedings of the National Academy of Sciences of
the United States of America 105: 2957-2962.
Matthey-Doret, R., and M. C. Whitlock, 2018 Background selection and the
statistics of population differentiation: consequences for detecting
local adaptation. Biorxiv: 1-5.
McCormack, J. E., H. Huang and L. L. Knowles, 2009 Sky Islands, pp.
841-843 in Encyclopedia of islands .
McDonald, J. H., and M. Kreitman, 1991 Adaptive protein evolution at the
Adh locus in Drosophila . Nature 351: 652-654.
McKenna, A., M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis et
al. , 2010 The Genome Analysis Toolkit: A MapReduce framework for
analyzing next-generation DNA sequencing data. Proceedings of the
International Conference on Intellectual Capital, Knowledge Management
& Organizational Learning 20: 1297-1303.
McVean, G., 2007 The structure of linkage disequilibrium around a
selective sweep. Genetics 175: 1395-1406.
Merkling, S. H., and R. P. van Rij, 2013 Beyond RNAi: Antiviral defense
strategies in Drosophila and mosquito. Journal of Insect
Physiology 59: 159-170.
Messer, P. W., and D. A. Petrov, 2012 The McDonald-Kreitman Test and its
Extensions under Frequent Adaptation: Problems and Solutions.
Proceedings of the National Academy of Sciences 110: 8615-8620.
Messer, P. W., and D. A. Petrov, 2013 Population genomics of rapid
adaptation by soft selective sweeps. Trends in Ecology & Evolution
28: 659-669.
Narasimhan, V., P. Danecek, A. Scally, Y. Xue, C. Tyler-Smith et
al. , 2016 BCFtools/RoH: A hidden Markov model approach for detecting
autozygosity from next-generation sequencing data. Bioinformatics
32: 1749-1751.
Nei, M., 1987 Molecular evolutionary genetics . Columbia
university press.
Nei, M., and J. Miller, 1990 A Simple Method for Estimating Average
Number of Nucleotide Substitutions Within and Between Populations From
Restriction Data. Genetics 125: 873-879.
Noor, M. a. F., D. a. Garfield, S. W. Schaeffer and C. a. Machado, 2007
Divergence between the Drosophila pseudoobscura and D.
persimilis genome sequences in relation to chromosomal inversions.
Genetics 177: 1417-1428.
Palmer, W. H., J. Joosten, G. J. Overheul, P. W. Jansen, M. Vermeulenet al. , 2018 Induction and suppression of NF- κB signalling by a
DNA virus of Drosophila.
Parmesan, C., and G. Yohe, 2003 A globally coherent fingerprint of
climate change impacts across natural systems. Nature 421:37-42.
Petrov, D. a., A.-S. Fiston-Lavier, M. Lipatov, K. Lenkov and J.
González, 2011 Population genomics of transposable elements inDrosophila melanogaster. Molecular Biology and Evolution
28: 1633-1644.
Pool, J., and C. H. Langley, 2013 DPGP3.
Pool, J. E., R. B. Corbett-detig, R. P. Sugino, K. A. Stevens, C. M.
Cardeno et al. , 2012 Population Genomics of Sub-SaharanDrosophila melanogaster: African Diversity and Non-African
Admixture. PLoS Genetics 8: 1-24.
Porretta, D., V. Mastrantonio, R. Bellini, P. Somboon and S. Urbanelli,
2012 Glacial history of a modern invader: phylogeography and species
distribution modelling of the Asian tiger mosquito Aedes albopictus.
PLoS One 7: e44515.
Rankin, M. A., and J. C. A. Burchsted, 1992 The Cost of Migration in
Insects. Annual Review of Entymology 37: 533-559.
Rastogi, S., and D. a. Liberles, 2005 Subfunctionalization of duplicated
genes as a transition state to neofunctionalization. BMC evolutionary
biology 5: 28.
Rausch, T., T. Zichner, A. Schlattl, A. M. Stutz, V. Benes et
al. , 2012 DELLY: structural variant discovery by integrated paired-end
and split-read analysis. Bioinformatics 28: i333-i339.
Rosenzweig, C., D. Karoly, M. Vicarelli, P. Neofotis, Q. Wu et
al. , 2008 Attributing physical and biological impacts to anthropogenic
climate change. Nature 453: 353-357.
Schrider, D. R., D. Houle, M. Lynch and M. W. Hahn, 2013 Rates and
genomic consequences of spontaneous mutational events in Drosophila
melanogaster. Genetics 194: 937-954.
Searle, J. B., P. Kotlik, R. V. Rambau, S. Markova, J. S. Hermanet al. , 2009 The Celtic fringe of Britain: insights from small
mammal phylogeography. Proc Biol Sci 276: 4287-4294.
Smit, A. F. A., and R. Hubley, 2008 RepeatModeler Open-1.0.
Smit, A. F. A., and R. Hubley, 2013-2015 RepeatMasker Open-4.0, pp.
RepeatMasker.
Smith, F. A., J. L. Betancourt and J. H. Brown, 1995 Evolution of Body
Size in the Woodrat Over the Past 25,000 Years of Climate Change.
Science 270: 2012-2014.
Smith, N. G. C., and A. Eyre-Walker, 2002 Adaptive protein evolution inDrosophila . Nature 415: 1022-1024.
Stajich, J. E., and M. W. Hahn, 2005 Disentangling the effects of
demography and selection in human history. Mol Biol Evol 22:63-73.
Stoletzki, N., and A. Eyre-Walker, 2011 Estimation of the neutrality
index. Molecular Biology and Evolution 28: 63-70.
Subramanian, A., P. Tamayo, V. K. Mootha, S. Mukherjee, B. L. Ebertet al. , 2005 Gene set enrichment analysis: A knowledge-based
approach for interpreting genome-wide expression profiles. PNAS
102: 15545–15550.
Survey, A. G., 2005 Arizona Geology. Arizona Geology 35: 1-6.
Tajima, F., 1989 Statistical method for testing the neutral mutation
hypothesis by DNA polymorphism. Genetics 123: 585-595.
Takeda, K., and S. Akira, 2005 Toll-like receptors in innate immunity.
International Immunology 17: 1-14.
Unckless, R. L., 2011a A DNA Virus of Drosophila . PLoS ONE
6: e26564.
Unckless, R. L., 2011b The potential role of the X chromosome in the
emergence of male-killing from mutualistic endosymbionts. J Theor Biol
291: 99-104.
Unckless, R. L., and J. Jaenike, 2011 Maintenance of a Male-KillingWolbachia in Drosophila innubila By Male-Killing Dependent
and Male-Killing Independent Mechanisms. Evolution 66: 678-689.
Walsh, D. B., M. P. Bolda, R. E. Goodhue, A. J. Dreves, J. Lee et
al. , 2011 Drosophila suzukii (Diptera: Drosophilidae ):
Invasive Pest of Ripening Soft Fruit Expanding its Geographic Range and
Damage Potential. Journal of Integrated Pest Management 2: 1-7.
Watanabe, T. K., O. Yamaguchi and T. Mukai, 1974 The Genetic Variability
of Third Chromosomes in a Local Population of Drosophila
melanogaster . Genetics 82: 63-82.
Weir, B. S., and C. C. Cockerham, 1984 Estimating F-Statistics for the
Analysis of Population Structure. Evolution 38: 1358-1370.
White, T. A., S. E. Perkins, G. Heckel and J. B. Searle, 2013 Adaptive
evolution during an ongoing range expansion: the invasive bank vole
(Myodes glareolus ) in Ireland. Mol Ecol 22: 2971-2985.
Wright, S. I., B. Lauga and D. Charlesworth, 2003 Subdivision and
haplotype structure in natural populations of Arabidopsis lyrata .
Molecular Ecology 12: 1247–1263.
Ye, K., M. H. Schulz, Q. Long, R. Apweiler and Z. Ning, 2009 Pindel : a
pattern growth approach to detect break points of large deletions and
medium sized insertions from paired-end short reads. Bioinformatics
25: 2865-2871.
Zambon, R. A., M. Nandakumar, V. N. Vakharia and L. P. Wu, 2005 The Toll
pathway is important for an antiviral response in Drosophila .
Proceedings of the National Academy of Sciences 102: 7257-7262.