Thursday, February 2, 2023
HomeScienceHigh heterogeneity in genomic differentiation between phenotypically divergent songbirds: a test of...

High heterogeneity in genomic differentiation between phenotypically divergent songbirds: a test of mitonuclear co-introgression

  • Alcaide M, Scordato ESC, Price TD, Irwin DE (2014) Genomic divergence in a ring species complex. Nature 511:83–85

    PubMed 

    Google Scholar 

  • Alström P, Olsson U, Lei F, Wang H, Gao W, Sundberg P (2008) Phylogeny and classification of the old world Emberizini (Aves, Passeriformes). Mol Phylogenet Evol 47:960–973

    PubMed 

    Google Scholar 

  • Alves PC, Melo-Ferreira J, Freitas H, Boursot P (2008) The ubiquitous mountain hare mitochondria: Multiple introgressive hybridization in hares, genus Lepus. Philos Trans R Soc B 363:2831–2839

    Google Scholar 

  • Avise JC (2000) Phylogeography: The history and formation of species. Harvard University Press, Cambridge, Mass

  • Ballard JWO, Melvin RG, Katewa SD, Maas K (2007) Mitochondrial DNA variation is associated with measurable differences in life-history traits and mitochondrial metabolism in Drosophila simulans. Evolution 61:1735–1747

    PubMed 

    Google Scholar 

  • Barreto FS, Watson ET, Lima TG, Willett CS, Edmands S, Li W et al. (2018) Genomic signatures of mitonuclear coevolution across populations of Tigriopus californicus. Nat Ecol Evol 2:1250–1257

    PubMed 

    Google Scholar 

  • Barrientos A, Müller S, Dey R, Wienberg J, Moraes CT (2000) Cytochrome c oxidase assembly in primates is sensitive to small evolutionary variations in amino acid sequence. Mol Biol Evol 17:1508–1519

    PubMed 

    Google Scholar 

  • Baute GJ, Owens GL, Bock DG, Rieseberg LH (2016) Genome‐wide genotyping‐by‐sequencing data provide a high‐resolution view of wild Helianthus diversity, genetic structure, and interspecies gene flow. Am J Bot 103:2170–2177

    PubMed 

    Google Scholar 

  • Beck EA, Thompson AC, Sharbrough J, Brud E, Llopart A (2015) Gene flow between Drosophila yakuba and Drosophila santomea in subunit V of cytochrome c oxidase: A potential case of cytonuclear cointrogression. Evolution 69:1973–1986

    PubMed 
    PubMed Central 

    Google Scholar 

  • Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120

    PubMed 
    PubMed Central 

    Google Scholar 

  • Borge T, Webster MT, Andersson G, Saetre G (2005) Contrasting patterns of polymorphism and divergence on the Z chromosome and autosomes in two Ficedula flycatcher species. Genetics 171:1861–1873

    PubMed 
    PubMed Central 

    Google Scholar 

  • Burton RS, Barreto FS (2012) A disproportionate role for mtDNA in Dobzhansky–Muller incompatibilities? Mol Ecol 21:4942–4957

    PubMed 

    Google Scholar 

  • Bryson J, Robert W, De Oca AN, Jaeger JR, Riddle BR (2010) Elucidation of cryptic diversity in a widespread Nearctic treefrog reveals episodes of mitochondrial gene capture as frogs diversified across a dynamic landscape. Evolution 64:2315–2330

    PubMed 

    Google Scholar 

  • Calvo SE, Mootha VK (2010) The mitochondrial proteome and human disease. Annu Rev Genom. Hum Genet 11:25–44

    Google Scholar 

  • Coyne JA, Orr HA (2004) Speciation. Sinauer Associates, Sunderland, Mass

  • Cruickshank TE, Hahn MW (2014) Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow. Mol Ecol 23:3133–3157

    PubMed 

    Google Scholar 

  • Cutter AD, Payseur BA (2013) Genomic signatures of selection at linked sites: unifying the disparity among species. Nat Rev Genet 14:262–274

    PubMed 
    PubMed Central 

    Google Scholar 

  • Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA et al. (2011) The variant call format and VCFtools. Bioinformatics 27:2156–2158

    PubMed 
    PubMed Central 

    Google Scholar 

  • Dean R, Zimmer F, Mank JE (2014) The potential role of sexual conflict and sexual selection in shaping the genomic distribution of mito-nuclear genes. Genome Biol Evol 6:1096–1104

    PubMed 
    PubMed Central 

    Google Scholar 

  • Diodato D, Ghezzi D, Tiranti V (2014) The mitochondrial aminoacyl tRNA synthetases: Genes and syndromes. Int J Cell Biol 2014:1–11

    Google Scholar 

  • Drown DM, Preuss KM, Wade MJ (2012) Evidence of a paucity of genes that interact with the mitochondrion on the X in mammals. Genome Biol Evol 4:763–880

    PubMed 

    Google Scholar 

  • Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES et al. (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PloS ONE 6:e19379

    PubMed 
    PubMed Central 

    Google Scholar 

  • Ernster L, Schatz G (1981) Mitochondria: A historical review. J Cell Biol 91:227s–255s

    PubMed 

    Google Scholar 

  • Gascuel O (1997) BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol 14:685–695

    PubMed 

    Google Scholar 

  • Geraldes A, Askelson KK, Nikelski E, Doyle FI, Harrower WL, Winker K et al. (2019) Population genomic analyses reveal a highly differentiated and endangered genetic cluster of northern goshawks (Accipiter gentilis laingi) in Haida Gwaii. Evol Appl 12:757–772

    PubMed 
    PubMed Central 

    Google Scholar 

  • Gershoni M, Levin L, Ovadia O, Toiw Y, Shani N, Dadon S et al. (2014) Disrupting mitochondrial-nuclear coevolution affects OXPHOS complex I integrity and impacts human health. Genome Biol Evol 6:2665–2680

    PubMed 
    PubMed Central 

    Google Scholar 

  • Gershoni M, Templeton AR, Mishmar D (2009) Mitochondrial bioenergetics as a major motive force of speciation. BioEssays 31:642–650

    PubMed 

    Google Scholar 

  • Greber BJ, Ban N (2016) Structure and function of the mitochondrial ribosome. Annu Rev Biochem 85:103–132

    PubMed 

    Google Scholar 

  • Harr B (2006) Genomic islands of differentiation between house mouse subspecies. Genome Res 16:730–737

    PubMed 
    PubMed Central 

    Google Scholar 

  • Hebert PD, Penton EH, Burns JM, Janzen DH, Hallwachs W (2004) Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc Natl Acad Sci USA 101:14812–14817

    PubMed 
    PubMed Central 

    Google Scholar 

  • Hejase HA, Salman-Minkov A, Campagna L, Hubisz MJ, Lovette IJ, Gronau I et al. (2020) Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps. Proc Natl Acad Sci USA 117:30554–30565

    PubMed 
    PubMed Central 

    Google Scholar 

  • Hill GE, (2019a) Reconciling the mitonuclear compatibility species concept with rampant mitochondrial introgression Integr Comp Biol 59:912–924

  • Hill GE (2019b) Mitonuclear Ecology (First ed.). Oxford University Press, Oxford

  • Hill GE (2020) Genetic hitchhiking, mitonuclear coadaptation, and the origins of mt DNA barcode gaps. Ecol Evol 10:9048–9059

    PubMed 
    PubMed Central 

    Google Scholar 

  • Hulsey CD, Bell KL, García‐de‐León FJ, Nice CC, Meyer A (2016) Do relaxed selection and habitat temperature facilitate biased mitogenomic introgression in a narrowly endemic fish? Ecol Evol 6:3684–3698

    PubMed 
    PubMed Central 

    Google Scholar 

  • Irwin DE (2018) Sex chromosomes and speciation in birds and other ZW systems. Mol Ecol 27:3831–3851

    PubMed 

    Google Scholar 

  • Irwin DE, Alcaide M, Delmore KE, Irwin JH, Owens GL (2016) Recurrent selection explains parallel evolution of genomic regions of high relative but low absolute differentiation in a ring species. Mol Ecol 25:4488–4507

    PubMed 

    Google Scholar 

  • Irwin DE, Milá B, Toews DPL, Brelsford A, Kenyon HL, Porter AN et al. (2018) A comparison of genomic islands of differentiation across three young avian species pairs. Mol Ecol 27:4839–4855

    PubMed 

    Google Scholar 

  • Irwin DE, Rubtsov AS, Panov EN (2009) Mitochondrial introgression and replacement between yellowhammers (Emberiza citrinella) and pine buntings (Emberiza leucocephalos) (Aves: Passeriformes). Biol J Linn Soc 98:422–438

    Google Scholar 

  • Kerr KCR, Stoeckle MY, Dove CJ, Weigt LA, Francis CM, Hebert PDN (2007) Comprehensive DNA barcode coverage of North American birds. Mol Ecol Notes 7:535–543

    PubMed 
    PubMed Central 

    Google Scholar 

  • Kirkpatrick M (2010) How and why chromosome inversions evolve. PLoS Biol 8:e1000501

    PubMed 
    PubMed Central 

    Google Scholar 

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

    PubMed 
    PubMed Central 

    Google Scholar 

  • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N et al. (2009) The sequence alignment map format and SAMtools. Bioinformatics 25:2078–2079

    PubMed 
    PubMed Central 

    Google Scholar 

  • Llopart A, Herrig D, Brud E, Stecklein Z (2014) Sequential adaptive introgression of the mitochondrial genome in Drosophila yakuba and Drosophila santomea. Mol Ecol 23:1124–1136

    PubMed 
    PubMed Central 

    Google Scholar 

  • Lotz C, Lin AJ, Black CM, Zhang J, Lau E, Deng N et al. (2014) Characterization, design, and function of the mitochondrial proteome: From organs to organisms. J Proteome Res 13:433–446

    PubMed 

    Google Scholar 

  • Lu J, Wu C (2005) Weak selection revealed by the whole-genome comparison of the X chromosome and autosomes of human and chimpanzee. Proc Natl Acad Sci 102:4063–4067

    PubMed 
    PubMed Central 

    Google Scholar 

  • Lynch M, Koskella B, Schaack S (2006) Mutation pressure and the evolution of organelle genomic architecture. Science 311:1727–1730

    PubMed 

    Google Scholar 

  • Mank JE, Nam K, Ellegren H (2010) Faster-Z evolution is predominantly due to genetic drift. Mol Biol Evol 27:661–670

    PubMed 

    Google Scholar 

  • Manthey JD, Geiger M, Moyle RG (2017) Relationships of morphological groups in the northern flicker superspecies complex (Colaptes auratus & C. chrysoides). Syst Biodivers 15:183–191

    Google Scholar 

  • McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A et al. (2010) The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303

    PubMed 
    PubMed Central 

    Google Scholar 

  • Meisel RP, Connallon T (2013) The faster-X effect: Integrating theory and data. Trends Genet 29:537–544

    PubMed 
    PubMed Central 

    Google Scholar 

  • Moore WS (1995) Inferring phylogenies from mtDNA variation: Mitochondrial-gene trees versus nuclear-gene trees. Evolution 49:718–726

    PubMed 

    Google Scholar 

  • Morales HE, Pavlova A, Amos N, Major R, Kilian A, Greening C et al. (2018) Concordant divergence of mitogenomes and a mitonuclear gene cluster in bird lineages inhabiting different climates. Nat Ecol Evol 2:1258–1267

    PubMed 

    Google Scholar 

  • Nadeau NJ, Whibley A, Jones RT, Davey JW, Dasmahapatra KK, Baxter SW et al. (2012) Genomic islands of divergence in hybridizing Heliconius butterflies identified by large-scale targeted sequencing. Philos Trans R Soc B 367:343–353

    Google Scholar 

  • Osada N, Akashi H (2012) Mitochondrial-nuclear interactions and accelerated compensatory evolution: Evidence from the primate cytochrome c oxidase complex. Mol Biol Evol 29:337–346

    PubMed 

    Google Scholar 

  • Panov EN, Rubtsov AS, Monzikov DG (2003) Hybridization between yellowhammer and pine bunting in Russia. Dutch Bird 25:17–31

    Google Scholar 

  • Panov EN, Rubtsov AS, Mordkovich MV (2007) New data on the relationships between two species of buntings (Emberiza citrinella and E. leucocephalos) hybridizing in the areas of overlap of their ranges. Zool Zh 86:1362–1378

    Google Scholar 

  • Paradis E, Schliep K (2019) Ape 5.0: An environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 35:526–528

    PubMed 

    Google Scholar 

  • Price T (2008) Speciation in birds. Roberts and Co, Greenwood Village, Colo

  • R Core Team (2014) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria, http://www.r-project.org/

    Google Scholar 

  • Rubtsov AS (2007) Variability of songs of the yellowhammer (Emberiza citrinella) and pine bunting (Emberiza leucocephala) as an evidence of population structure and evolutionary history of the species. Zool Zh 86:863–876

    Google Scholar 

  • Rubtsov AS, Opaev AS (2012) Phylogeny reconstruction of the yellowhammer (Emberiza citrinella) and pine bunting (Emberiza leucocephala) based on song and morphological characters. Biol Bull Russ Acad Sci 39:715–728

    Google Scholar 

  • Rubtsov AS, Tarasov VV (2017) Relations between the yellowhammer (Emberiza citrinella) and the pine bunting (Emberiza leucocephalos) in the forested steppe of the Trans-Urals. Biol Bull 44:1059–1072

    Google Scholar 

  • Ruegg K, Anderson EC, Boone J, Pouls J, Smith TB (2014) A role for migration-linked genes and genomic islands in divergence of a songbird. Mol Ecol 23:4757–4769

    PubMed 

    Google Scholar 

  • Sackton TB, Corbett-Detig RB, Nagaraju J, Vaishna L, Arunkumar KP, Hartl DL (2014) Positive selection drives faster-z evolution in silkmoths. Evolution 68:2331–2342

    PubMed 
    PubMed Central 

    Google Scholar 

  • Sackton TB, Haney RA, Rand DM (2003) Cytonuclear coadaptation in Drosophila: Disruption of cytochrome c oxidase activity in backcross genotypes. Evolution 57:2315–2325

    PubMed 

    Google Scholar 

  • Saraste M (1999) Oxidative phosphorylation at the fin de siècle. Science 283:1488–1493

    PubMed 

    Google Scholar 

  • Scordato ESC, Wilkins MR, Semenov G, Rubtsov AS, Kane NC, Safran RJ (2017) Genomic variation across two barn swallow hybrid zones reveals traits associated with divergence in sympatry and allopatry. Mol Ecol 26:5676–5691

    PubMed 

    Google Scholar 

  • Sloan DB, Havird JC, Sharbrough J (2017) The on-again, off-again relationship between mitochondrial genomes and species boundaries. Mol Ecol 26:2212–2236

    PubMed 
    PubMed Central 

    Google Scholar 

  • Sloan DB, Triant DA, Wu M, Taylor DR (2014) Cytonuclear interactions and relaxed selection accelerate sequence evolution in organelle ribosomes. Mol Biol Evol 31:673–682

    PubMed 

    Google Scholar 

  • Smukowski CS, Noor MAF (2011) Recombination rate variation in closely related species. Heredity 107:496–508

    PubMed 
    PubMed Central 

    Google Scholar 

  • Stacklies W, Redestig H, Scholz M, Walther D, Selbig J (2007) PcaMethods-a bioconductor package providing PCA methods for incomplete data. Bioinformatics 23:1164–1167

    PubMed 

    Google Scholar 

  • Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595

    PubMed 
    PubMed Central 

    Google Scholar 

  • Thornton K, Long M (2002) Rapid divergence of gene duplicates on the Drosophila melanogaster X chromosome. Mol Biol Evol 19:918–925

    PubMed 

    Google Scholar 

  • Toews DPL, Brelsford A (2012) The biogeography of mitochondrial and nuclear discordance in animals. Mol Ecol 21:3907–3930

    PubMed 

    Google Scholar 

  • Turner S (2018) Qqman: An R package for visualizing GWAS results using Q-Q and Manhattan plots. J Open Source Softw 3:731

    Google Scholar 

  • Wang S, Ore MJ, Mikkelsen EK, Lee-Yaw J, Toews DPL, Rohwer S et al. (2021) Signatures of mitonuclear coevolution in a warbler species complex. Nat Commun 12:4279–4279

    PubMed 
    PubMed Central 

    Google Scholar 

  • Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A et al. (2010) The genome of a songbird. Nature 464:757–762

    PubMed 
    PubMed Central 

    Google Scholar 

  • Weir BS, Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38:1358–1370

    PubMed 

    Google Scholar 

  • Wu C (2001) The genic view of the process of speciation. J Evol Biol 14:851–865

    Google Scholar 

  • Yannic G, Dubey S, Hausser J, Basset P (2010) Additional data for nuclear DNA give new insights into the phylogenetic position of Sorex granarius within the Sorex araneus group. Mol Phylogenet Evol 57:1062–1071

    PubMed 

    Google Scholar 

  • Abdullah Anaman
    Abdullah Anamanhttps://aanaman.me
    I am a highly competent IT professional with a proven track record in designing websites, building apps etc. I have strong technical skills as well as excellent interpersonal skills, enabling me to interact with a wide range of clients.
    RELATED ARTICLES

    LEAVE A REPLY

    Please enter your comment!
    Please enter your name here
    Captcha verification failed!
    CAPTCHA user score failed. Please contact us!

    Most Popular

    Recent Comments