Evidence for mtDNA capture in the jacamar Galbula leucogastra/chalcothorax species-complex and insights on the evolution of white-sand ecosystems in the Amazon basin
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Adeney, 2016, White-sand ecosystems in amazonia, Biotropica, 48, 7, 10.1111/btp.12293
Alonso, 2001, A new Zimmerius tyrannulet (Aves: Tyrannidae) from white sand forests of northern Amazonian Peru, Wilson Bull., 113, 1, 10.1676/0043-5643(2001)113[0001:ANZTAT]2.0.CO;2
Anderson, 1981, White-sand vegetation of Brazilian Amazonia, Biotropica, 13, 199, 10.2307/2388125
Arruda, 2018, Vegetation cover of Brazil in the last 21 ka: new insights into the Amazonian refugia and Pleistocenic arc hypotheses, Global Ecol. Biogeogr., 27, 47, 10.1111/geb.12646
Avise, 2009, Phylogeography: retrospect and prospect, J. Biogeogr., 36, 3, 10.1111/j.1365-2699.2008.02032.x
Avise, 1987, Intraspecific phylogeography: The mitochondrial DNA bridge between population genetics and systematics, Ann. Rev. Ecol. Syst., 18, 489, 10.1146/annurev.es.18.110187.002421
Barthe, 2017, Tropical rainforest that persisted: inferences from the Quaternary demographic history of eight tree species in the Guiana Shield, Mol. Ecol., 26, 1161, 10.1111/mec.13949
Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170
Bonnet, 2017, A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes, Evolution, 71, 2140, 10.1111/evo.13296
Borges, 2003, Species poor but distinct: bird assemblages in white sand vegetation in Jaú National Park, Brazilian Amazon, Ibis, 146, 114, 10.1111/j.1474-919X.2004.00230.x
Borges, 2016, Bird communities in Amazonian white-sand vegetation patches: effects of landscape configuration and biogeographic context, Biotropica, 48, 121, 10.1111/btp.12296
Borges, 2016, What is the avifauna of Amazonian white-sand vegetation, Bird Conserv. Int., 26, 192, 10.1017/S0959270915000052
Bouckaert, 2014, BEAST 2: a software platform for Bayesian evolutionary analysis, PLoS Comput. Biol., 10, e1003537, 10.1371/journal.pcbi.1003537
Bock, 2014, On the adaptive value of cytoplasmic genomes in plants, Mol. Ecol., 23, 4899, 10.1111/mec.12920
Brown, 1977, Evolution in Modern Amazonian Non-Forest Islands: Heliconius hermathena, Biotropica, 9, 95, 10.2307/2387664
Burney, 2009, Ecology predicts levels of genetic differentiation in neotropical birds, Am. Nat., 174, 358, 10.1086/603613
Bush, 2017, Climate science: the resilience of Amazonian forests, Nature, 541, 167, 10.1038/541167a
Campbell, 2006, The Pan-Amazonian Ucayali Peneplain, late Neogene sedimentation in Amazonia, and the birth of the modern Amazon River system, Palaeogeogr. Palaeoclimatol. Palaeoecol., 239, 166, 10.1016/j.palaeo.2006.01.020
Capurucho, 2013, Combining phylogeography and landscape genetics of Xenopipo atronitens (Aves: Pipridae), a white sand campina specialist, to understand Pleistocene landscape evolution in Amazonia, Biol. J. Linn. Soc., 110, 60, 10.1111/bij.12102
Carling, 2008, Haldane's rule in an avian system: using cline theory and divergence population genetics to test for differential introgression of mitochondrial, autosomal, and sex-linked loci across the Passerina bunting hybrid zone, Evolution, 62, 2600, 10.1111/j.1558-5646.2008.00477.x
Cheng, 2013, Climate change patterns in Amazonia and biodiversity, Nat. Commun., 4, 1411, 10.1038/ncomms2415
Clement, 2000, TCS: a computer program to estimate gene genealogies, Mol. Ecol., 9, 1657, 10.1046/j.1365-294x.2000.01020.x
Cohn-Haft, M., 2008. Estudos temático de impacto da BR-319: Aves. Internal Report. INPA, Manaus, Brazil.
Cohn-Haft, 2013, A new species of Herpsilochmus antwren from west of the Rio Madeira in Amazonian Brazil, 272
Cohn-Haft, 2013, A new species of Cyanocorax jay from savannas of the central Amazon, 306
Cordeiro, 2016, Impact of sedimentary processes on white-sand vegetation in an Amazonian megafan, J. Trop. Ecol., 32, 498, 10.1017/S0266467416000493
Cowling, 2001, Paleovegetation simulations of Lowland Amazonia and implications for neotropical allopatry and speciation, Quat. Res., 55, 140, 10.1006/qres.2000.2197
Daly-Engel, 2012, Global phylogeography with mixed-marker analysis reveals male-mediated dispersal in the endangered scalloped hammerhead shark (Sphyrna lewini), PloS one, 7, e29986, 10.1371/journal.pone.0029986
Dias, 2018, Mitochondrial introgression obscures phylogenetic relationships among manakins of the genus Lepidothrix (Aves: Pipridae), Mol Phylogenet. Evolution, 126, 314, 10.1016/j.ympev.2018.04.017
Dobler, 2014, A meta-analysis of the strength and nature of cytoplasmic genetic effects, J. Evol. Biol., 27, 2021, 10.1111/jeb.12468
Drovetski, 2015, Effects of asymmetric nuclear introgression, introgressive mitochondrial sweep, and purifying selection on phylogenetic reconstruction and divergence estimates in the Pacific clade of Locustella warblers, PloS One, 10, e0122590, 10.1371/journal.pone.0122590
Drummond, 2012, Bayesian phylogenetics with BEAUti and the BEAST 1.7, Mol. Biol. Evol., 29, 1969, 10.1093/molbev/mss075
Espurt, 2010, The Nazca Ridge and uplift of the Fitzcarrald Arch: implication for regional geology in northern South America, 89
Excoffier, 2009, Genetic consequences of range expansions, Ann. Rev. Ecol. Evol. Syst., 40, 481, 10.1146/annurev.ecolsys.39.110707.173414
Faircloth, B.C., 2013. Illumiprocessor: a trimmomatic wrapper for parallel adapter and quality trimming. https://doi.org/10.6079/J9ILL.
Faircloth, 2016, PHYLUCE is a software package for the analysis of conserved genomic loci, Bioinformatics, 32, 786, 10.1093/bioinformatics/btv646
Faircloth, 2012, Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales, Syst. Biol., 61, 717, 10.1093/sysbio/sys004
Fernandes, 2013, Fine-scale endemism of Amazonian birds in a threatened landscape, Biodivers. Conserv., 22, 2683, 10.1007/s10531-013-0546-9
Fernandes, 2014, Rivers acting as barriers for bird dispersal in the Amazon, Rev. Bras. Ornitol., 22, 363, 10.1007/BF03544273
Ferreira, 2017, Biogeography of the Neotropical genus Malacoptila (Aves: Bucconidae): the influence of the Andean orogeny, Amazonian drainage evolution and palaeoclimate, J. Biogeogr., 44, 748, 10.1111/jbi.12888
Fine, 2016, Habitat endemism in white-sand forests: Insights into the mechanisms of lineage diversification and community assembly of the Neotropical Flora, Biotropica, 48, 24, 10.1111/btp.12301
Fine, 2010, A Floristic Study of the White-Sand Forests of Peru, Ann. Missouri Bot. Gard., 97, 283, 10.3417/2008068
Frasier, 2008, Amazonian lowland, white sand areas as ancestral regions for South American biodiversity: Biogeographic and phylogenetic patterns in Potalia (Angiospermae: Gentianaceae), Org. Divers. Evol., 8, 44, 10.1016/j.ode.2006.11.003
Funk, 2003, Species-level paraphyly and polyphyly: Frequency, causes, and consequences, with insights from animal mitochondrial DNA, Ann. Rev. Ecol. Evol. Syst., 34, 397, 10.1146/annurev.ecolsys.34.011802.132421
Gatesy, 2014, Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum, Mol. Phylogenet. Evol., 80, 231, 10.1016/j.ympev.2014.08.013
Grabherr, 2011, Full-length transcriptome assembly from RNA-Seq data without a reference genome, Nat. Biotechnol., 29, 644, 10.1038/nbt.1883
Griscom, 1941, Birds of Lower Amazonia, Bull. Mus. Comp. Zool., 88, 83
Haffer, 1974
Hailer, 2012, Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage, Science, 336, 344, 10.1126/science.1216424
Harvey, 2016, Sequence capture versus restriction site associated DNA sequencing for shallow systematics, Syst. Biol., 65, 910, 10.1093/sysbio/syw036
Harvey, 2017, Habitat association predicts genetic diversity and population divergence in Amazonian birds, Am. Nat., 190, 631, 10.1086/693856
Hill, 2017, The mitonuclear compatibility species concept, Auk, 134, 393, 10.1642/AUK-16-201.1
Hoorn, 1993, Marine incursions and the influence of Andean tectonics on the Miocene depositional history of northwestern Amazonia: results of a palynostratigraphic study, Palaeogeogr. Palaeoclimatol. Palaeoecol., 105, 267, 10.1016/0031-0182(93)90087-Y
Hoorn, 2010, Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity, Science, 330, 927, 10.1126/science.1194585
Hulsey, 2016, Do relaxed selection and habitat temperature facilitate biased mitogenomic introgression in a narrowly endemic fish?, Ecol. Evol., 6, 3684, 10.1002/ece3.2121
Katoh, 2013, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol. Biol. Evol., 30, 772, 10.1093/molbev/mst010
Kearse, 2012, Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data, Bioinformatics, 28, 1647, 10.1093/bioinformatics/bts199
Kubatko, 2007, Inconsistency of phylogenetic estimates from concatenated data under coalescence, Syst. Biol., 56, 17, 10.1080/10635150601146041
Lanfear, 2017, PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses, Mol. Biol. Evol., 34, 772
Langmead, 2012, Fast gapped-read alignment with Bowtie 2, Nat. Methods, 9, 357, 10.1038/nmeth.1923
Langmead, 2009, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol., 10, R25, 10.1186/gb-2009-10-3-r25
Laranjeiras, T.O., Naka, L.N., Bechtold, C.L., Costa, T.V.V., Andretti, C.B., Cerqueira, M.C., Torres, M.d.F., Rodrigues, G.L., Santos, M.P.D., Vargas, C.F., Pacheco, A.M.F., Sardelli, C.H., Mazar-Barnett, J., Cohn-Haft, M., 2014. The avifauna of Viruá National Park, Roraima, reveals megadiversity in northern Amazonia. Rev. Bras. Ornitol. 22, 138–171.
Latrubesse, 2002, Evidence of Quaternary palaeohydrological changes in middle Amazonia: the Aripuanã-Roosevelt and Jiparaná “fans”, Z. Geomorph. N F, 129, 61
Levey, 1992, Evolutionary precursors of long-distance migration: resource availability and movement patterns in Neotropical landbirds, Am. Nat., 140, 447, 10.1086/285421
Llopart, 2014, Sequential adaptive introgression of the mitochondrial genome in Drosophila yakuba and Drosophila santomea, Mol. Ecol., 23, 1124, 10.1111/mec.12678
Manthey, 2016, Comparison of target-capture and restriction-site associated DNA sequencing for phylogenomics: a test in Cardinalid Tanagers (Aves, Genus: Piranga), Syst. Biol., 65, 640, 10.1093/sysbio/syw005
Matos, 2016, Comparative phylogeography of two bird species, Tachyphonus phoenicius (Thraupidae) and Polytmus theresiae (Trochilidae), specialized in Amazonian White-sand vegetation, Biotropica, 48, 110, 10.1111/btp.12292
Mayle, 2004, Responses of Amazonian ecosystems to climatic and atmospheric carbon dioxide changes since the last glacial maximum, Philos. Trans. R. Soc. Lond. B Biol. Sci., 359, 499, 10.1098/rstb.2003.1434
McCormack, 2013, Applications of next-generation sequencing to phylogeography and phylogenetics, Mol. Phylogenet. Evol., 66, 526, 10.1016/j.ympev.2011.12.007
McGuire, 2014, Molecular phylogenetics and the diversification of hummingbirds, Curr. Biol., 24, 910, 10.1016/j.cub.2014.03.016
McKay, 2010, The causes of mitochondrial DNA gene tree paraphyly in birds, Mol. Phylogenet. Evol., 54, 647, 10.1016/j.ympev.2009.08.024
Moore, 1995, Inferring phylogenies from mtDNA variation: mitochondrial-gene trees versus nuclear-gene trees, Evolution, 49, 718
Moyle, 2016, Tectonic collision and uplift of Wallacea triggered the global songbird radiation, Nat. Commun., 7, 12709, 10.1038/ncomms12709
Nascimento, 2004, Podzolization as a deferralitization process: a study of an Acrisol-Podzol sequence derived from Palaeozoic sandstones in the northern upper Amazon Basin, Eur. J. Soil Sci., 55, 523, 10.1111/j.1365-2389.2004.00616.x
Nogueira, 2013, Neogene-Quaternary sedimentary and paleovegetation history of the eastern Solimões Basin, central Amazon region, J. South Am. Earth Sci., 46, 89, 10.1016/j.jsames.2013.05.004
Ogilvie, 2017, StarBEAST2 brings faster species tree inference and accurate estimates of substitution rates, Mol. Biol. Evol., 34, 2101, 10.1093/molbev/msx126
Oliver, 2013, Microevolutionary processes generate phylogenomic discordance at ancient divergences, Evolution, 67, 1823, 10.1111/evo.12047
Orr, 1996, Dobzhansky, Bateson, and the genetics of speciation, Genetics, 144, 1331, 10.1093/genetics/144.4.1331
Parker, 1987, Fifty-two Amazonian bird species new to Bolivia, Bull. Brit. Orn. Cl., 107, 94
Peters, 1948
Pomara, 2012, Avian composition co-varies with floristic composition and soil nutrient concentration in Amazonian upland forests, Biotropica, 44, 545, 10.1111/j.1744-7429.2011.00851.x
Prance, 1978, Notes on the vegetation of Amazonia I. A preliminary note on the origin of the open white sand campinas of the lower Rio Negro, Brittonia, 30, 60, 10.2307/2806458
Prum, 2015, A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing, Nature, 526, 569, 10.1038/nature15697
Rambaut, A., Suchard, M.A., Xie, D., Drummond, A.J., 2014. Tracer v1.6. http://beast.bio.ed.ac.uk/Tracer.
Rheindt, F.E., Christidis, L., Norman, J.A., 2008. Habitat shifts in the evolutionary history of a Neotropical flycatcher lineage from forest and open landscapes. BMC Evol. Biol. 8.
Rheindt, 2011, Genetic introgression: an Integral but neglected component of speciation in birds, Auk, 128, 620, 10.1525/auk.2011.128.4.620
Ribas, 2012, A palaeobiogeographic model for biotic diversification within Amazonia over the past three million years, Proc. Biol. Sci., 279, 681
Roddaz, 2005, Forebulge dynamics and environmental control in Western Amazonia: the case study of the Arch of Iquitos (Peru), Tectonophysics, 399, 87, 10.1016/j.tecto.2004.12.017
Ronquist, 2012, MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space, Syst. Biol., 61, 539, 10.1093/sysbio/sys029
Sambrook, J., Russel, D.W., 2001. Molecular Cloning: A laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
Sauer, 2007, Podzol: Soil of the year 2007. A review on its genesis, occurrence, and functions, J. Plant Nutr. Soil Sci., 170, 581, 10.1002/jpln.200700135
Shipham, 2015, Phylogenetic analysis of the Australian rosella parrots (Platycercus) reveals discordance among molecules and plumage, Mol. Phylogenet. Evol., 91, 150, 10.1016/j.ympev.2015.05.012
Shipham, 2017, A genomic approach reinforces a hypothesis of mitochondrial capture in eastern Australian rosellas, Auk, 134, 181, 10.1642/AUK-16-31.1
Sloan, 2017, The on-again, off-again relationship between mitochondrial genomes and species boundaries, Mol. Ecol., 26, 2212, 10.1111/mec.13959
Smith, 2014, Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales, Syst. Biol., 63, 83, 10.1093/sysbio/syt061
Sorenson, 1999, Primers for a PCR-based approach to mitochondrial genome sequencing in birds and other vertebrates, Mol. Phylogenet. Evol., 12, 105, 10.1006/mpev.1998.0602
Stamatakis, 2014, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, 30, 1312, 10.1093/bioinformatics/btu033
Stotz, 1996
Thom, 2015, Cryptic speciation in the white-shouldered antshrike (Thamnophilus aethiops, Aves - Thamnophilidae): the tale of a transcontinental radiation across rivers in lowland Amazonia and the northeastern Atlantic Forest, Mol. Phylogenet. Evol., 82, 95, 10.1016/j.ympev.2014.09.023
Tobias, J.A., 2017. Jacamars (Galbulidae). In: del Hoyo, J., Elliot, A., Sargatal, J. (Eds.), Handbook of the birds of the world. Lynx Ediciones, Barcelona. Retrieved from http://www.hbw.com/node/52281 on 15 August 2017.
Toews, 2012, The biogeography of mitochondrial and nuclear discordance in animals, Mol. Ecol., 21, 3907, 10.1111/j.1365-294X.2012.05664.x
Vicentini, 2016, The evolutionary history of Pagamea (Rubiaceae), a white-sand specialist lineage in tropical South America, Biotropica, 48, 58, 10.1111/btp.12295
Vriesendorp, C., Pitman, N.C., Rojas Moscoso, J.I., Pawlak, B.A., Chavéz, L.R., Méndez, L.C., Collantes, M.V., Rimachi, E.P.F., 2006. Perú: Matsés. Rapid biological inventories report 16. The Field Museum, Chicago.
Wang, 2017, Ancestral range reconstruction of Galliformes: the effects of topology and taxon sampling, J. Biogeogr., 44, 122, 10.1111/jbi.12782
Weir, 2008, Calibrating the avian molecular clock, Mol. Ecol., 17, 2321, 10.1111/j.1365-294X.2008.03742.x
Weisrock, 2012, Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics, Mol. Biol. Evol., 29, 1615, 10.1093/molbev/mss008
Whitney, 1998, A new Herpsilochmus antwren (Aves: Thamnophilidae) from Northern Amazonian Peru and adjacent Ecuador: the role of edaphic heterogeneity of terra firme forest, Auk, 115, 559, 10.2307/4089406
Whitney, 2005, A new species of Gnatcatcher from white-sand forests of northern Amazonian Peru with revision of the Polioptila guianensis complex, Wilson Bull., 117, 113, 10.1676/04-064
Witt, 2004, 132
Zink, 2008, Mitochondrial DNA under siege in avian phylogeography, Mol. Ecol., 17, 2107, 10.1111/j.1365-294X.2008.03737.x