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Species delimitation and mitonuclear discordance within a species complex of biting midges

  • 1.

    De Queiroz, K. Species concepts and species delimitation. Syst. Biol. 56, 879–886. https://doi.org/10.1080/10635150701701083 (2007).

    Article 
    PubMed 

    Google Scholar 

  • 2.

    Coyne, J. A. & Orr, H. A. Speciation (Sinauer Associates Inc, 2004).

    Google Scholar 

  • 3.

    Endler, J. A. Gene flow and population differentiation: studies of clines suggest that differentiation along environmental gradients may be independent of gene flow. Science 179, 243–250 (1973).

    CAS 
    PubMed 
    ADS 

    Google Scholar 

  • 4.

    Mayr, E. Systematics and the Origin of Species, from the Viewpoint of a Zoologist (Harvard University Press, 1999).

    Google Scholar 

  • 5.

    Richardson, J. L., Urban, M. C., Bolnick, D. I. & Skelly, D. K. Microgeographic adaptation and the spatial scale of evolution. Trends Ecol. Evol. 29, 165–176 (2014).

    PubMed 

    Google Scholar 

  • 6.

    Nosil, P. Ernst Mayr and the integration of geographic and ecological factors in speciation. Biol. J. Lin. Soc. 95, 26–46 (2008).

    Google Scholar 

  • 7.

    Kisel, Y. & Barraclough, T. G. Speciation has a spatial scale that depends on levels of gene flow. Am. Nat. 175, 316–334 (2010).

    PubMed 

    Google Scholar 

  • 8.

    Leliaert, F. et al. DNA-based species delimitation in algae. Eur. J. Phycol. 49, 179–196 (2014).

    Google Scholar 

  • 9.

    Carstens, B. C., Pelletier, T. A., Reid, N. M. & Satler, J. D. How to fail at species delimitation. Mol. Ecol. 22, 4369–4383 (2013).

    PubMed 

    Google Scholar 

  • 10.

    Schlick-Steiner, B. C. et al. Integrative taxonomy: a multisource approach to exploring biodiversity. Annu. Rev. Entomol. 55, 421–438 (2010).

    CAS 
    PubMed 

    Google Scholar 

  • 11.

    Capblancq, T., Mavárez, J., Rioux, D. & Després, L. Speciation with gene flow: evidence from a complex of alpine butterflies (Coenonympha, Satyridae). Ecol. Evol. 9, 6444–6457 (2019).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 12.

    Pedraza-Marrón, C. d. R. et al. Genomics overrules mitochondrial DNA, siding with morphology on a controversial case of species delimitation. Proc. R. Soc. B 286, 20182924 (2019).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 13.

    Hinojosa, J. C. et al. A mirage of cryptic species: genomics uncover striking mitonuclear discordance in the butterfly Thymelicus sylvestris. Mol. Ecol. 28, 3857–3868 (2019).

    PubMed 

    Google Scholar 

  • 14.

    Nygren, A. et al. A mega-cryptic species complex hidden among one of the most common annelids in the North East Atlantic. PLoS ONE 13, e0198356 (2018).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 15.

    Thielsch, A., Knell, A., Mohammadyari, A., Petrusek, A. & Schwenk, K. Divergent clades or cryptic species? Mito-nuclear discordance in a Daphnia species complex. BMC Evol. Biol. 17, 1–9 (2017).

    Google Scholar 

  • 16.

    Eyer, P. A. & Hefetz, A. Cytonuclear incongruences hamper species delimitation in the socially polymorphic desert ants of the Cataglyphis albicans group in Israel. J. Evol. Biol. 31, 1828–1842 (2018).

    CAS 
    PubMed 

    Google Scholar 

  • 17.

    Borkent, A. Biology of Disease Vectors. 2nd edn, i–xxiii + 1–785 (Elsevier Academic Press, 2004).

  • 18.

    Mellor, P., Boorman, J. & Baylis, M. Culicoides biting midges: their role as arbovirus vectors. Annu. Rev. Entomol. 45, 307–340 (2000).

    CAS 
    PubMed 

    Google Scholar 

  • 19.

    Rushton, J. & Lyons, N. Economic impact of Bluetongue: a review of the effects on production. Veterinaria italiana 51, 401–406 (2015).

    PubMed 

    Google Scholar 

  • 20.

    Tabachnick, W. J. Culicoides vriipennis and Bluetongue-Virus eidemiology in the United States. Annu. Rev. Entomol. 41, 23–43. https://doi.org/10.1146/annurev.en.41.010196.000323 (1996).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 21.

    Wirth, W. W. & Jones, R. H. The North American Subspecies of Culicoides variipennis (Diptera, Heleidae). U. S. Dep. Agric. Tech. Bull 1170, 1–35 (1957).

    Google Scholar 

  • 22.

    Holbrook, F. R. et al. Sympatry in the Culicoides variipennis Complex (Diptera: Ceratopogonidae): a Taxonomic Reassessment. J. Med. Entomol. 37, 65–76. https://doi.org/10.1603/0022-2585-37.1.65 (2000).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 23.

    Hopken, M. W. Pathogen Vectors at the Wildlife-Livestock Interface: Molecular Approaches to Elucidating Culicoides (Diptera: Ceratopogonidae) Biology (University of Colorado, 2016).

    Google Scholar 

  • 24.

    Shults, P. A Study of the Taxonomy, Ecology, and Systematics of Culicoides Species (Diptera: Ceratopogonidae) Including those Associated with Deer Breeding Facilities in Southeast Texas (Texas A&M University, 2015).

    Google Scholar 

  • 25.

    Velten, R. K. & Mullens, B. A. Field morphological variation and laboratory hybridization of Culicoides variipennis sonorensis and C. v. occidentalis (Diptera:Ceratopogonidae) in southern California. J. Med. Entomol. 34, 277–284 (1997).

    CAS 
    PubMed 

    Google Scholar 

  • 26.

    Fontaine, M. C. et al. Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science 347, 1258522 (2015).

    PubMed 

    Google Scholar 

  • 27.

    Bolnick, D. I. & Otto, S. P. The magnitude of local adaptation under genotype-dependent dispersal. Ecol. Evol. 3, 4722–4735 (2013).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 28.

    Slatkin, M. Isolation by distance in equilibrium and non-equilibrium populations. Evolution 47, 264–279 (1993).

    PubMed 

    Google Scholar 

  • 29.

    Pante, E. et al. Species are hypotheses: avoid connectivity assessments based on pillars of sand. Mol. Ecol. 24, 525–544 (2015).

    PubMed 

    Google Scholar 

  • 30.

    Jacquet, S. et al. Colonization of the Mediterranean basin by the vector biting midge species Culicoides imicola: an old story. Mol. Ecol. 24, 5707–5725. https://doi.org/10.1111/mec.13422 (2015).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 31.

    Onyango, M. G. et al. Genotyping of whole genome amplified reduced representation libraries reveals a cryptic population of Culicoides brevitarsis in the Northern Territory, Australia. BMC Genomics 17, 769. https://doi.org/10.1186/s12864-016-3124-1 (2016).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 32.

    Onyango, M. G. et al. Delineation of the population genetic structure of Culicoides imicola in East and South Africa. Parasit. Vectors 8, 660. https://doi.org/10.1186/s13071-015-1277-4 (2015).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 33.

    Mignotte, A. et al. High dispersal capacity of Culicoides obsoletus (Diptera: Ceratopogonidae), vector of bluetongue and Schmallenberg viruses, revealed by landscape genetic analyses. Parasit. Vectors 14, 1–14 (2021).

    Google Scholar 

  • 34.

    Sanders, C. J. & Carpenter, S. Assessment of an immunomarking technique for the study of dispersal of Culicoides biting midges. Infect. Genet. Evol. 28, 583–587 (2014).

    PubMed 

    Google Scholar 

  • 35.

    Kluiters, G., Swales, H. & Baylis, M. Local dispersal of palaearctic Culicoides biting midges estimated by mark-release-recapture. Parasit. Vectors 8, 86 (2015).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 36.

    Ducheyne, E. et al. Quantifying the wind dispersal of Culicoides species in Greece and Bulgaria. Geospat. Health 10, 177–189 (2007).

    Google Scholar 

  • 37.

    Purse, B. V. et al. Climate change and the recent emergence of bluetongue in Europe. Nat. Rev. Microbiol. 3, 171–181 (2005).

    CAS 
    PubMed 

    Google Scholar 

  • 38.

    Jacquet, S. et al. Range expansion of the Bluetongue vector, Culicoides imicola, in continental France likely due to rare wind-transport events. Sci. Rep. https://doi.org/10.1038/srep27247 (2016).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 39.

    Rundle, H. D. & Nosil, P. Ecological speciation. Ecol. Lett. 8, 336–352 (2005).

    Google Scholar 

  • 40.

    Wang, I. J. & Bradburd, G. S. Isolation by environment. Mol. Ecol. 23, 5649–5662 (2014).

    PubMed 

    Google Scholar 

  • 41.

    Shults, P. A Study of Culicoides Biting Midges in the Subgenus Monoculicoides: Population Genetics, Taxonomy, Systematics, and Control. Ph.D. thesis, Texas A&M University (2021).

  • 42.

    Jewiss-Gaines, A., Barelli, L. & Hunter, F. F. First records of Culicoides sonorensis (Diptera: Ceratopogonidae), a known vector of bluetongue virus, Southern Ontario. J. Med. Entomol. 54, 757–762. https://doi.org/10.1093/jme/tjw215 (2017).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 43.

    Chan, K. M. & Levin, S. A. Leaky prezygotic isolation and porous genomes: rapid introgression of maternally inherited DNA. Evolution 59, 720–729 (2005).

    CAS 
    PubMed 

    Google Scholar 

  • 44.

    Harrison, R. G. Hybrid zones: windows on evolutionary process. Oxf. Surv. Evol. Biol. 7, 69–128 (1990).

    Google Scholar 

  • 45.

    Harrison, R. G. Animal mitochondrial DNA as a genetic marker in population and evolutionary biology. Trends Ecol. Evol. 4, 6–11 (1989).

    CAS 
    PubMed 

    Google Scholar 

  • 46.

    Després, L. One, Two or More Species? Mitonuclear Discordance and Species Delimitation. Molecular ecology 28(17), 3845–3847 (2019).

    PubMed 

    Google Scholar 

  • 47.

    Janes, J. K. et al. The K= 2 conundrum. Mol. Ecol. 26, 3594–3602 (2017).

    PubMed 

    Google Scholar 

  • 48.

    De Meester, L., Vanoverbeke, J., Kilsdonk, L. J. & Urban, M. C. Evolving perspectives on monopolization and priority effects. Trends Ecol. Evol. 31, 136–146 (2016).

    PubMed 

    Google Scholar 

  • 49.

    Ballard, J. W. O., Chernoff, B. & James, A. C. Divergence of mitochondrial DNA is not corroborated by nuclear DNA, morphology, or behavior in Drosophila simulans. Evolution 56, 527–545 (2002).

    PubMed 

    Google Scholar 

  • 50.

    Behura, S., Sahu, S., Mohan, M. & Nair, S. Wolbachia in the Asian rice gall midge, Orseolia oryzae (Wood-Mason): Correlation between host mitotypes and infection status. Insect Mol. Biol. 10, 163–171 (2001).

    CAS 
    PubMed 

    Google Scholar 

  • 51.

    Covey, H. et al. Cryptic Wolbachia (Rickettsiales: Rickettsiaceae) detection and prevalence in Culicoides (Diptera: Ceratopogonidae) midge populations in the United States. J. Med. Entomol. 57, 1262–1269. https://doi.org/10.1093/jme/tjaa003 (2020).

    Article 
    PubMed 

    Google Scholar 

  • 52.

    Pagès, N., Muñoz-Muñoz, F., Verdún, M., Pujol, N. & Talavera, S. First detection of Wolbachia-infected Culicoides (Diptera: Ceratopogonidae) in Europe: Wolbachia and Cardinium infection across Culicoides communities revealed in Spain. Parasit. Vectors 10, 582. https://doi.org/10.1186/s13071-017-2486-9 (2017).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 53.

    Pilgrim, J. et al. Cardinium symbiosis as a potential confounder of mtDNA based phylogeographic inference in Culicoides imicola (Diptera: Ceratopogonidae), a vector of veterinary viruses. Parasit. Vectors 14, 100. https://doi.org/10.1186/s13071-020-04568-3 (2021).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 54.

    Hare, M. P. Prospects for nuclear gene phylogeography. Trends Ecol. Evol. 16, 700–706 (2001).

    Google Scholar 

  • 55.

    Onyango, M. G. et al. Assessment of population genetic structure in the arbovirus vector midge, Culicoides brevitarsis (Diptera: Ceratopogonidae), using multi-locus DNA microsatellites. Vet. Res. 46, 108. https://doi.org/10.1186/s13567-015-0250-8 (2015).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 56.

    Fonseca, D. M., Smith, J. L., Kim, H.-C. & Mogi, M. Population genetics of the mosquito Culex pipiens pallens reveals sex-linked asymmetric introgression by Culex quinquefasciatus. Infect. Genet. Evol. 9, 1197–1203 (2009).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 57.

    Goubert, C., Minard, G., Vieira, C. & Boulesteix, M. Population genetics of the Asian tiger mosquito Aedes albopictus, an invasive vector of human diseases. Heredity 117, 125–134 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 58.

    Lehmann, T. et al. Microgeographic structure of Anopheles gambiae in western Kenya based on mtDNA and microsatellite loci. Mol. Ecol. 6, 243–253 (1997).

    CAS 
    PubMed 

    Google Scholar 

  • 59.

    Chapuis, M.-P. & Estoup, A. Microsatellite null alleles and estimation of population differentiation. Mol. Biol. Evol. 24, 621–631. https://doi.org/10.1093/molbev/msl191 (2006).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 60.

    Manni, M. et al. Molecular markers for analyses of intraspecific genetic diversity in the Asian Tiger mosquito, Aedes albopictus. Parasit. Vectors 8, 1–11 (2015).

    Google Scholar 

  • 61.

    Arntzen, J. W., Jehle, R., Bardakci, F., Burke, T. & Wallis, G. P. Asymmetric viability of reciprocal-cross hybrids between Crested and Marbled Newts (Triturus cristatus and T. marmoratus). Evolution 63, 1191–1202. https://doi.org/10.1111/j.1558-5646.2009.00611.x (2009).

    Article 
    PubMed 

    Google Scholar 

  • 62.

    Gibeaux, R. et al. Paternal chromosome loss and metabolic crisis contribute to hybrid inviability in Xenopus. Nature 553, 337. https://doi.org/10.1038/nature25188 (2018).

    CAS 
    Article 
    PubMed 
    PubMed Central 
    ADS 

    Google Scholar 

  • 63.

    Werren, J. H., Baldo, L. & Clark, M. E. Wolbachia: master manipulators of invertebrate biology. Nat. Rev. Microbiol. 6, 741 (2008).

    CAS 
    PubMed 

    Google Scholar 

  • 64.

    Servedio, M. R. & Kirkpatrick, M. The effects of gene flow on reinforcement. Evolution 51, 1764–1772. https://doi.org/10.1111/j.1558-5646.1997.tb05100.x (1997).

    Article 
    PubMed 

    Google Scholar 

  • 65.

    Howard, D. J. Reinforcement: origin, dynamics, and fate of an evolutionary hypothesis. Hybrid zones and the evolutionary process, 46–69 (1993).

  • 66.

    Yukilevich, R. Asymmetrical patterns of speciation uniquely support reinforcement in Drosophila. Evolution 66, 1430–1446. https://doi.org/10.1111/j.1558-5646.2011.01534.x (2012).

    Article 
    PubMed 

    Google Scholar 

  • 67.

    Downes, J. A. The Culicoides variipennis complex: a necessary re-alignment of nomenclature (Diptera: Ceratopogonidae). Can. Entomol. 110, 63–69 (1978).

    Google Scholar 

  • 68.

    Toews, D. P. & Brelsford, A. The biogeography of mitochondrial and nuclear discordance in animals. Mol. Ecol. 21, 3907–3930 (2012).

    CAS 
    PubMed 

    Google Scholar 

  • 69.

    Smith, H. & Mullens, B. A. Seasonal activity, size, and parity of Culicoides occidentalis (Diptera: Ceratopogonidae) in a coastal southern California salt marsh. J. Med. Entomol. 40, 352–355. https://doi.org/10.1603/0022-2585-40.3.352 (2003).

    Article 
    PubMed 

    Google Scholar 

  • 70.

    Linley, J. The effect of salinity on oviposition and egg hatching in Culicoides variipennis sonorensis (Diptera: Ceratopogonidae). J. Am. Mosq. Control Assoc. 2, 79–82 (1986).

    CAS 
    PubMed 

    Google Scholar 

  • 71.

    Gerry, A. C. & Mullens, B. A. Response of Male Culicoides variipennis sonorensis (Diptera: Ceratopogonidae) to carbon dioxide and observations of mating behavior on and near cattle. J. Med. Entomol. 35, 239–244. https://doi.org/10.1093/jmedent/35.3.239 (1998).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 72.

    Nolan, D. V. et al. Rapid diagnostic PCR assays for members of the Culicoides obsoletus and Culicoides pulicaris species complexes, implicated vectors of bluetongue virus in Europe. Vet. Microbiol. 124, 82–94 (2007).

    CAS 
    PubMed 

    Google Scholar 

  • 73.

    Sebastiani, F. et al. Molecular differentiation of the Old World Culicoides imicola species complex (Diptera, Ceratopogonidae), inferred using random amplified polymorphic DNA markers. Mol. Ecol. 10, 1773–1786 (2001).

    CAS 
    PubMed 

    Google Scholar 

  • 74.

    Carlson, D. Identification of mosquitoes of Anopheles gambiae species complex A and B by analysis of cuticular components. Science 207, 1089–1091 (1980).

    CAS 
    PubMed 
    ADS 

    Google Scholar 

  • 75.

    Palacios, G. et al. Characterization of the Sandfly fever Naples species complex and description of a new Karimabad species complex (genus Phlebovirus, family Bunyaviridae). J. Gen. Virol. 95, 292 (2014).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 76.

    Rivas, G., Souza, N. & Peixoto, A. A. Analysis of the activity patterns of two sympatric sandfly siblings of the Lutzomyia longipalpis species complex from Brazil. Med. Vet. Entomol. 22, 288–290 (2008).

    CAS 
    PubMed 

    Google Scholar 

  • 77.

    Wilson, W. C. et al. Current status of bluetongue virus in the Americas. Bluetongue 10, 197–220 (2009).

    Google Scholar 

  • 78.

    Allen, S. E. et al. Epizootic Hemorrhagic Disease in White-Tailed Deer, Canada. Emerg. Infect. Dis. 25, 832–834. https://doi.org/10.3201/eid2504.180743 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 79.

    McGregor, B. L. et al. Field data implicating Culicoides stellifer and Culicoides venustus (Diptera: Ceratopogonidae) as vectors of epizootic hemorrhagic disease virus. Parasit. Vectors 12, 258. https://doi.org/10.1186/s13071-019-3514-8 (2019).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 80.

    Shults, P., Ho, A., Martin, E. M., McGregor, B. L. & Vargo, E. L. Genetic diversity of Culicoides stellifer (Diptera: Ceratopogonidae) in the Southeastern United States compared with sequences from Ontario, Canada. J. Med. Entomol. 57, 1324–1327. https://doi.org/10.1093/jme/tjaa025 (2020).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 81.

    Mallet, J. Hybridization as an invasion of the genome. Trends Ecol. Evol. 20, 229–237 (2005).

    PubMed 

    Google Scholar 

  • 82.

    Ciota, A. T., Chin, P. A. & Kramer, L. D. The effect of hybridization of Culex pipiens complex mosquitoes on transmission of West Nile virus. Parasit. Vectors 6, 1–4 (2013).

    Google Scholar 

  • 83.

    Meiswinkel, R., Gomulski, L., Delécolle, J., Goffredo, M. & Gasperi, G. The taxonomy of Culicoides vector complexes-unfinished business. Vet. Ital. 40, 151–159 (2004).

    CAS 
    PubMed 

    Google Scholar 

  • 84.

    Ewels, P., Magnusson, M., Lundin, S. & Käller, M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics (Oxford, England) 32, 3047–3048. https://doi.org/10.1093/bioinformatics/btw354 (2016).

    CAS 
    Article 

    Google Scholar 

  • 85.

    Andrews, S. Babraham bioinformatics-FastQC a quality control tool for high throughput sequence data. https://www.bioinformatics.babraham.ac.uk/projects/fastqc (2010).

  • 86.

    Rochette, N. C., Rivera-Colón, A. G. & Catchen, J. M. Stacks 2: Analytical methods for paired-end sequencing improve RADseq-based population genomics. Mol. Ecol. 28, 4737–4754 (2019).

    CAS 
    PubMed 

    Google Scholar 

  • 87.

    Morales-Hojas, R. et al. The genome of the biting midge Culicoides sonorensis and gene expression analyses of vector competence for bluetongue virus. BMC Genomics 19, 624. https://doi.org/10.1186/s12864-018-5014-1 (2018).

    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 88.

    Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (Oxford, England) 25, 1754–1760 (2009).

    CAS 

    Google Scholar 

  • 89.

    Pante, E. et al. Use of RAD sequencing for delimiting species. Heredity 114, 450–459 (2015).

    CAS 
    PubMed 

    Google Scholar 

  • 90.

    Benestan, L. M. et al. Conservation genomics of natural and managed populations: building a conceptual and practical framework. Mol. Ecol. 25, 2967–2977 (2016).

    PubMed 

    Google Scholar 

  • 91.

    Lischer, H. E. & Excoffier, L. PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics (Oxford, England) 28, 298–299 (2012).

    CAS 

    Google Scholar 

  • 92.

    Pina-Martins, F., Silva, D. N., Fino, J. & Paulo, O. S. Structure_threader: An improved method for automation and parallelization of programs structure, fastStructure and MavericK on multicore CPU systems. Mol. Ecol. Resour. 17, e268–e274 (2017).

    CAS 
    PubMed 

    Google Scholar 

  • 93.

    Raj, A., Stephens, M. & Pritchard, J. K. Variational Inference of Population Structure in Large SNP Datasets. bioRxiv 10, 001073 (2013).

    Google Scholar 

  • 94.

    R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.http://www.R-project.org/ (2013).

  • 95.

    Jombart, Thibaut, and Caitlin Collins. A tutorial for discriminant analysis of principal components (DAPC) using adegenet 2.0. 0. London: Imperial College London, MRC Centre for Outbreak Analysis and Modelling (2015).

  • 96.

    Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics (Oxford, England) 30, 1312–1313 (2014).

    CAS 

    Google Scholar 

  • 97.

    Leaché, A. D., Banbury, B. L., Felsenstein, J., De Oca, A.N.-M. & Stamatakis, A. Short tree, long tree, right tree, wrong tree: New acquisition bias corrections for inferring SNP phylogenies. Syst. Biol. 64, 1032–1047 (2015).

    PubMed 
    PubMed Central 

    Google Scholar 

  • 98.

    Pattengale, N. D., Alipour, M., Bininda-Emonds, O. R., Moret, B. M. & Stamatakis, A. How many bootstrap replicates are necessary?. J. Comput. Biol. 17, 337–354 (2010).

    MathSciNet 
    CAS 
    PubMed 

    Google Scholar 

  • 99.

    Trifinopoulos, J., Nguyen, L.-T., von Haeseler, A. & Minh, B. Q. W-IQ-TREE: A fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res. 44, W232–W235 (2016).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 100.

    Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K., Von Haeseler, A. & Jermiin, L. S. ModelFinder: Fast model selection for accurate phylogenetic estimates. Nat. Methods 14, 587–589 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 101.

    Nguyen, L.-T., Schmidt, H. A., Von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).

    CAS 
    PubMed 

    Google Scholar 

  • 102.

    Hoang, D. T., Chernomor, O., Von Haeseler, A., Minh, B. Q. & Vinh, L. S. UFBoot2: improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 35, 518–522 (2018).

    CAS 
    PubMed 

    Google Scholar 

  • 103.

    Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 30. Syst. Biol. 59, 307–321. https://doi.org/10.1093/sysbio/syq010 (2010).

    CAS 
    Article 
    PubMed 

    Google Scholar 

  • 104.

    Rousset, F. genepop’007: a complete re‐implementation of the genepop software for Windows and Linux. Molecular ecology resources 8(1), 103–106 (2008).

    Google Scholar 

  • 105.

    Rousset, F. Genetic differentiation between individuals. J Evol Biol 13, 58–62 (2000).

    Google Scholar 

  • 106.

    Loiselle, B. A., Sork, V. L., Nason, J. & Graham, C. Spatial genetic structure of a tropical understory shrub, Psychotria officinalis (Rubiaceae). Am. J. Bot. 82, 1420–1425 (1995).

    Google Scholar 

  • 107.

    Hardy, O. & Vekemans, X. SPAGeDi 1.5. A program for Spatial Pattern Analysis of Genetic Diversity. User’s manual http://ebe.ulb.ac.be/ebe/SPAGeDi_files/SPAGeDi_1.5_Manual.pdf. Université Libre de Bruxelles, Brussells, Belgium.[Google Scholar] (2015).

  • 108.

    Jay, F., Sjödin, P., Jakobsson, M. & Blum, M. G. Anisotropic isolation by distance: the main orientations of human genetic differentiation. Mol. Biol. Evol. 30, 513–525 (2013).

    CAS 
    PubMed 

    Google Scholar 

  • 109.

    Piry, S. et al. Mapping Averaged Pairwise Information (MAPI): a new exploratory tool to uncover spatial structure. Methods Ecol. Evol. 7, 1463–1475 (2016).

    Google Scholar 

  • 110.

    Kearse, M. et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics (Oxford, England) 28, 1647–1649. https://doi.org/10.1093/bioinformatics/bts199 (2012).

    Article 

    Google Scholar 

  • 111.

    Hopken, M. W. Pathogen Vectors at The Wildlife-Livestock Interface: Molecular Approaches to Elucidating Culicoides (Diptera: Ceratopogonidae) Ph.D. thesis, Colorado State University (2016).

  • 112.

    Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35, 1547–1549 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • 113.

    Bandelt, H. J., Forster, P. & Rohl, A. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol. 16, 37–48. https://doi.org/10.1093/oxfordjournals.molbev.a026036 (1999).

    CAS 
    Article 
    PubMed 

    Google Scholar 


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