Brodie, J., Maggs, C. A., & John, D. M. Inexperienced seaweeds of Britain and Eire. pp. 242 (British Phycological Society, 2007).
Leliaert, F. et al. Phylogeny and molecular evolution of the inexperienced algae. Crit. Rev. Plant Sci. 31, 1–46 (2012).
Del Cortona, A. & Leliaert, F. Molecular evolution and morphological diversification of ulvophytes (Chlorophyta). Perspect. Phycol. 5, 27–43 (2018).
Fang, L., Leliaert, F., Zhang, Z., Penny, D. & Zhong, B. Evolution of the Chlorophyta: Insights from chloroplast phylogenomic analyses. J. Syst. Evol. 55, 322–332 (2017).
Prazukin, A. V., Anufriieva, E. V. & Shadrin, N. V. Is biomass of filamentous inexperienced algae Cladophora spp. (Chlorophyta, Ulvophyceae) a limiteless low-cost and helpful useful resource for medication and pharmacology? A overview. Rev. Aquacult. 12, 2493–2510 (2020).
Cocquyt, E., Verbruggen, H., Leliaert, F. & De Clerck, O. Evolution and cytological diversification of the inexperienced seaweeds (Ulvophyceae). Mol. Biol. Evol. 27, 2052–2061 (2010).
Atkinson, N. et al. Introducing an algal carbon-concentrating mechanism into greater vegetation: location and incorporation of key elements. Plant Biotechnol. J. 14, 1302–1315 (2016).
Mattox, Ok. R. & Stewart, Ok. D. Classification of the inexperienced algae: an idea primarily based on comparative cytology. In: Irvine, D. E. G. & John, D. M., editors. Systematics of the Inexperienced Algae. pp. 29–72 (Tutorial Press, 1984).
O’Kelly, C. J. & Floyd, G. L. Correlations amongst patterns of sporangial construction and growth, life histories, and ultrastructural options within the Ulvophyceae. In: Systematics of the Inexperienced Algae (eds Irvine, D. E. G. & John, D. M.) pp. 121–156 (Tutorial Press, 1984).
Van den Hoek, C., Stam, W. T. & Olsen, J. L. The emergence of a brand new chlorophytan system, and Dr. Kornmann’s contribution thereto. Helgol. Mar. Res. 42, 339–383 (1988).
Watanabe, S. & Nakayama, T. Ultrastructure and phylogenetic relationships of the unicellular inexperienced algae Ignatius tetrasporus and Pseudocharacium americanum (Chlorophyta). Phycol. Res. 55, 1–16 (2007).
Škaloud, P., Kalina, T., Nemjova, Ok., De Clerck, O. & Leliaert, F. Morphology and phylogenetic place of the freshwater inexperienced microalgae Chlorochytrium (Chlorophyceae) and Scotinosphaera (Scotinosphaerales, ord. nov., Ulvophyceae). J. Phycol. 49, 115–129 (2013).
Fučíková, Ok. et al. New phylogenetic hypotheses for the core Chlorophyta primarily based on chloroplast sequence knowledge. Entrance. Ecol. Evol. 2, 63 (2014).
Leliaert, F. & López-Bautista, J. M. The chloroplast genomes of Bryopsis plumosa and Tydemania expeditiones (Bryopsidales, Chlorophyta): compact genomes and genes of bacterial origin. BMC Genom. 16, 204 (2015).
Fang, L. et al. Enhancing phylogenetic inference of core Chlorophyta utilizing chloroplast sequences with robust phylogenetic indicators and heterogeneous fashions. Mol. Phylogenet. Evol. 127, 248–255 (2018).
Solar, L. et al. Chloroplast phylogenomic inference of inexperienced algae relationships. Sci. Rep. 6, 20528 (2016).
Li, X. et al. Giant phylogenomic datasets reveal deep relationships and trait evolution in chlorophyte inexperienced algae. Genome Biol. Evol. 13, evab101 (2021).
Del Cortona, A. et al. Neoproterozoic origin and a number of transitions to macroscopic progress in inexperienced seaweeds. Proc. Natl Acad. Sci. U.S.A. 117, 2551–2559 (2020).
Leebens-Mack, J. H. et al. One thousand plant transcriptomes and the phylogenomics of inexperienced vegetation. Nature 574, 679–685 (2019).
Gulbrandsen, Ø. S., Andresen, I. J., Krabberød, A. Ok., Bråte, J. & Shalchian-Tabrizi, Ok. Phylogenomic evaluation restructures the Ulvophyceae. J. Phycol. 57, 1223–1233 (2021).
Melton, J. R., Leliaert, F., Tronholm, A. & Lopez-Bautista, J. M. The whole chloroplast and mitochondrial genomes of the inexperienced macroalga Ulva sp. UNA00071828 (Ulvophyceae, Chlorophyta). PLoS ONE 10, e121020 (2015).
Javaux, E. J. & Knoll, A. H. Micropaleontology of the decrease Mesoproterozoic Roper Group, Australia, and implications for early eukaryotic evolution. J. Paleontol. 91, 199–229 (2017).
Moczydłowska, M., Touchdown, E. D., Zang, W. & Palacios, T. Proterozoic phytoplankton and timing of chlorophyte algae origins. Palaeontology 54, 721–733 (2011).
Butterfield, N. J., Knoll, A. H. & Swett, Ok. Paleobiology of the Neoproterozoic Svanbergfjellet Formation, Spitsbergen. Lethaia 27, 76–76 (1994).
LoDuca, S. T. New Ordovician marine macroalgae from North America, with observations on Buthograptus, Callithamnopsis, and Chaetocladus. J. Paleontol. 93, 197–214 (2018).
Verbruggen, H. et al. A multi-locus time-calibrated phylogeny of the siphonous inexperienced algae. Mol. Phylogenet. Evol. 50, 642–653 (2009).
Butterfield, N. J. Modes of pre-Ediacaran multicellularity. Precambrian Res. 173, 201–211 (2009).
Tang, Q., Pang, Ok., Yuan, X. & Xiao, S. A one-billion-year-old multicellular chlorophyte. Nat. Ecol. Evol. 4, 543–549 (2020).
Graham, L. E. Digging deeper: why we want extra Proterozoic algal fossils and how you can get them. J. Phycol. 55, 1–6 (2019).
Xiao, S. & Tang, Q. After the boring billion and earlier than the freezing hundreds of thousands: evolutionary patterns and improvements within the Tonian Interval. Emerg. Prime. Life Sci. 2, 161–171 (2018).
Rannala, B., Edwards, S. V., Leaché, A. & Yang, Z. The multi-species coalescent mannequin and species tree inference. Phylogenet. Genom. Period e-book part 3.3, pp. 3.3:1–21 (2020).
Liu, L., Wu, S. & Yu, L. Coalescent strategies for estimating species timber from phylogenomic knowledge. J. Syst. Evol. 53, 380–390 (2015).
Turmel, M., Otis, C. & Lemieux, C. Divergent copies of the big inverted repeat within the chloroplast genomes of ulvophycean inexperienced algae. Sci. Rep. 7, 994 (2017).
Leliaert, F. et al. Systematics of the marine microfilamentous inexperienced algae Uronema curvatum and Urospora microscopica (Chlorophyta). Eur. J. Phycol. 44, 487–496 (2009).
Del Cortona, A. et al. The plastid genome in Cladophorales inexperienced algae is encoded by hairpin chromosomes. Curr. Biol. 27, 3771–3782 (2017).
Smith, S. A., Moore, M. J., Brown, J. W. & Yang, Y. Evaluation of phylogenomic datasets reveals battle, concordance, and gene duplications with examples from animals and vegetation. BMC Evol. Biol. 15, 150 (2015).
Morales-Briones, D. F. et al. Disentangling sources of gene tree discordance in phylogenomic knowledge units: testing historical hybridizations in Amaranthaceae s.l. Syst. Biol. 70, 219–235 (2021).
Mirarab, S., Bayzid, M. S. & Warnow, T. Evaluating abstract strategies for multilocus species tree estimation within the presence of incomplete lineage sorting. Syst. Biol. 65, 366–380 (2016).
Pease, J. B., Brown, J. W., Walker, J. F., Hinchliff, C. E. & Smith, S. A. Quartet sampling distinguishes lack of assist from conflicting assist within the inexperienced plant tree of life. Am. J. Bot. 105, 385–403 (2018).
Jiang, X., Edwards, S. V. & Liu, L. The multispecies coalescent mannequin outperforms concatenation throughout numerous phylogenomic knowledge units. Syst. Biol. 69, 795–812 (2020).
Blom, M., Bragg, J. G., Potter, S. & Moritz, C. Accounting for uncertainty in gene tree estimation: summary-coalescent species tree inference in a difficult radiation of Australian lizards. Syst. Biol. 66, 352–366 (2017).
Liu, L., Xi, Z. & Davis, C. C. Coalescent strategies are sturdy to the simultaneous results of lengthy branches and incomplete lineage sorting. Mol. Biol. Evol. 32, 791–805 (2015).
Philippe, H. et al. Pitfalls in supermatrix phylogenomics. Eur. J. Taxon. 283, 1–25 (2017).
Crotty, S. M. et al. GHOST: recovering historic sign from heterotachously advanced sequence alignments. Syst. Biol. 69, 249–264 (2020).
Wang, H. C., Minh, B. Q., Susko, E. & Roger, A. J. Modeling web site heterogeneity with posterior imply web site frequency profiles accelerates correct phylogenomic estimation. Syst. Biol. 67, 216–235 (2018).
Brown, J. M. & Thomson, R. C. Evaluating mannequin efficiency in evolutionary biology. Annu. Rev. Ecol. Evol. Syst. 49, 95–114 (2018).
Foster, P. G. Modeling compositional heterogeneity. Syst. Biol. 53, 485–495 (2004).
Puttick, M. N. et al. The interrelationships of land vegetation and the character of the ancestral embryophyte. Curr. Biol. 28, 733–745 (2018).
Edwards, S. V. Is a brand new and common idea of molecular systematics rising? Evolution 63, 1–19 (2009).
Zhong, B., Liu, L., Yan, Z. & Penny, D. Origin of land vegetation utilizing the multispecies coalescent mannequin. Tendencies Plant Sci. 18, 492–495 (2013).
Yang, L. et al. Phylogenomic insights into deep phylogeny of angiosperms primarily based on broad nuclear gene sampling. Plant Commun. 1, 100027 (2020).
Yang, Y. et al. Prickly waterlily and inflexible hornwort genomes make clear early angiosperm evolution. Nat. Crops 6, 215–222 (2020).
Suh, A., Smeds, L. & Ellegren, H. The dynamics of incomplete lineage sorting throughout the traditional adaptive radiation of Neoavian birds. PLoS Biol. 13, e1002224 (2015).
Koenen, E. et al. Giant-scale genomic sequence knowledge resolve the deepest divergences within the legume phylogeny and assist a near-simultaneous evolutionary origin of all six subfamilies. N. Phytol. 225, 1355–1369 (2020).
Degnan, J. H. & Rosenberg, N. A. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Tendencies Ecol. Evol. 24, 332–340 (2009).
Tune, S., Liu, L., Edwards, S. V. & Wu, S. Resolving battle in eutherian mammal phylogeny utilizing phylogenomics and the multispecies coalescent mannequin. Proc. Natl Acad. Sci. U.S.A. 109, 14942–14947 (2012).
Cloutier, A. et al. Complete-genome analyses resolve the phylogeny of flightless birds (Palaeognathae) within the presence of an empirical anomaly zone. Syst. Biol. 68, 937–955 (2019).
Sauquet, H. A sensible information to molecular relationship. C. R. Palevol. 12, 355–367 (2013).
Ho, S. Y. W. & Phillips, M. J. Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence instances. Syst. Biol. 58, 367–380 (2009).
Parham, J. F. et al. Finest practices for justifying fossil calibrations. Syst. Biol. 61, 346–359 (2012).
Bykova, N. et al. Seaweeds by way of time: morphological and ecological evaluation of Proterozoic and early Paleozoic benthic macroalgae. Precambrian Res. 350, 105875 (2020).
LoDuca, S. T., Bykova, N., Wu, M., Xiao, S. & Zhao, Y. Seaweed morphology and ecology in the course of the nice animal diversification occasions of the early Paleozoic: a story of two floras. Geobiology 15, 588–616 (2017).
Sforna, M. C. et al. Intracellular certain chlorophyll residues determine 1 Gyr-old fossils as eukaryotic algae. Nat. Commun. 13, 146 (2022).
Jackson, C., Knoll, A. H., Chan, C. X. & Verbruggen, H. Plastid phylogenomics with broad taxon sampling additional elucidates the distinct evolutionary origins and timing of secondary inexperienced plastids. Sci. Rep. 8, 1523 (2018).
Strassert, J. F. H., Irisarri, I., Williams, T. A. & Burki, F. A molecular timescale for eukaryote evolution with implications for the origin of crimson algal-derived plastids. Nat. Commun. 12, 1879 (2021).
Nie, Y. et al. Accounting for uncertainty within the evolutionary timescale of inexperienced vegetation by way of clock-partitioning and fossil calibration methods. Syst. Biol. 69, 1–16 (2020).
Sánchez-Baracaldo, P., Raven, J. A., Pisani, D. & Knoll, A. H. Early photosynthetic eukaryotes inhabited low-salinity habitats. Proc. Natl Acad. Sci. U.S.A. 114, E7737–E7745 (2017).
Teyssèdre, B. Are the inexperienced algae (phylum Viridiplantae) two billion years previous? Carnets Géol. 3, CG2006 _A03 (2006).
Maloney, Ok. et al. New multicellular marine macroalgae from the early Tonian of northwestern Canada. Geology 49, 743–747 (2021).
Tang, Q. et al. The Proterozoic macrofossil Tawuia as a coenocytic eukaryote and a doable macroalga. Palaeogeogr. Palaeoclimatol. Palaeoecol. 576, 110485 (2021).
Ozaki, Ok., Reinhard, C. T. & Tajika, E. A sluggish mid-Proterozoic biosphere and its impact on Earth’s redox steadiness. Geobiology 17, 3–11 (2019).
Guilbaud, R., Poulton, S. W., Butterfield, N. J., Zhu, M. & Shields-Zhou, G. A. A worldwide transition to ferruginous situations within the early Neoproterozoic oceans. Nat. Geosci. 8, 466–470 (2015).
Brocks, J. et al. The rise of algae in Cryogenian oceans and the emergence of animals. Nature 548, 578–581 (2017).
Lyons, T. W., Reinhard, C. T. & Planavsky, N. J. The rise of oxygen in Earth’s early ocean and ambiance. Nature 506, 307–315 (2014).
Wang, X. et al. Oxygen, local weather and the chemical evolution of a 1400 million yr previous tropical marine setting. Am. J. Sci. 317, 861–900 (2017).
Zhang, Ok. et al. Oxygenation of the Mesoproterozoic ocean and the evolution of advanced eukaryotes. Nat. Geosci. 11, 345–350 (2018).
Sperling, E. A. et al. Redox heterogeneity of subsurface waters within the Mesoproterozoic ocean. Geobiology 12, 373–386 (2014).
Zhang, S. et al. Enough oxygen for animal respiration 1,400 million years in the past. Proc. Natl Acad. Sci. U.S.A. 113, 1731–1736 (2016).
Planavsky, N. J. et al. Low Mid-Proterozoic atmospheric oxygen ranges and the delayed rise of animals. Science 346, 635–638 (2014).
Grabherr, M. G. et al. Full-length transcriptome meeting from RNA-Seq knowledge with no reference genome. Nat. Biotechnol. 29, 644–652 (2011).
Davidson, N. M. & Oshlack, A. Corset: enabling differential gene expression evaluation for de novo assembled transcriptomes. Genome Biol. 15, 410 (2014).
Li, L., Stoeckert, C. J. & Roos, D. S. OrthoMCL: identification of ortholog teams for eukaryotic genomes. Genome Res 13, 2178–2189 (2003).
Petersen, M. et al. Orthograph: a flexible instrument for mapping coding nucleotide sequences to clusters of orthologous genes. BMC Bioinform. 18, 111 (2017).
Katoh, Ok. & Standley, D. M. MAFFT a number of sequence alignment software program model 7: enhancements in efficiency and usefulness. Mol. Biol. Evol. 30, 772–780 (2013).
Castresana, J. Collection of conserved blocks from a number of alignments for his or her use in phylogenetic evaluation. Mol. Biol. Evol. 17, 540–552 (2000).
Capella-Gutiérrez, S., Silla-Martinez, J. M. & Gabaldon, T. trimAl: a instrument for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).
Nguyen, L. T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: a quick and efficient stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).
Minh, B. Q., Nguyen, M. A. T. & von Haeseler, A. Ultrafast approximation for phylogenetic bootstrap. Mol. Biol. Evol. 30, 1188–1195 (2013).
Junier, T. & Zdobnov, E. M. The Newick utilities: high-throughput phylogenetic tree processing within the UNIX shell. Bioinformatics 26, 1669–1670 (2010).
Zhang, C., Rabiee, M., Sayyari, E. & Mirarab, S. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene timber. BMC Bioinform. 19, 153 (2018).
Guindon, S. et al. New algorithms and strategies to estimate maximum-likelihood phylogenies: assessing the efficiency of PhyML 3.0. Syst. Biol. 59, 307–321 (2010).
Guiry, M. D. & Guiry, G. M. AlgaeBase. World-wide digital publication, Nationwide College of Eire, Galway. https://www.algaebase.org (Accessed 22 March 2021).
Huerta-Cepas, J., Serra, F. & Bork, P. ETE 3: reconstruction, evaluation, and visualization of phylogenomic knowledge. Mol. Biol. Evol. 33, 1635–1638 (2016).
Wang, Ok. et al. Incomplete lineage sorting quite than hybridization explains the inconsistent phylogeny of the wisent. Commun. Biol. 1, 169 (2018).
Liu, L. & Yu, L. Phybase: an R bundle for species tree evaluation. Bioinformatics 26, 962–963 (2010).
Yang, Z. PAML 4: phylogenetic evaluation by most chance. Mol. Biol. Evol. 24, 1586–1591 (2007).
Smith, S. A., Brown, J. W. & Walker, J. F. So many genes, so little time: a sensible method to divergence-time estimation within the genomic period. PLoS ONE 13, e197433 (2018).
Reis, M. & Yang, Z. Approximate chance calculation on a phylogeny for Bayesian estimation of divergence instances. Mol. Biol. Evol. 28, 2161–2172 (2011).
Rambaut, A., Drummond, A. J., Xie, D., Baele, G. & Suchard, M. A. Posterior summarization in Bayesian phylogenetics utilizing Tracer 1.7. Syst. Biol. 67, 901–904 (2018).
Tao, Q., Barba-Montoya, J. & Kumar, S. Information-driven speciation tree prior for higher species divergence instances in calibration-poor molecular phylogenies. Bioinformatics 37, i102–i110 (2021).
Puttick, M. N. MCMCtreeR: features to arrange MCMCtree analyses and visualize posterior ages on timber. Bioinformatics 35, 5321–5322 (2019).
Lamb, D. M., Awramik, S. M., Chapman, D. J. & Zhu, S. Proof for eukaryotic diversification within the ∼1800 million-year-old Changzhougou Formation, North China. Precambrian Res. 173, 93–104 (2009).
Colbath, G. Ok. & Grenfell, H. R. Evaluation of organic affinities of Paleozoic acid-resistant, organic-walled eukaryotic algal microfossils (together with “acritarchs”). Rev. Palaeobot. Palynol. 86, 287–314 (1995).
Nye, E., Feist-Burkhardt, S., Horne, D. J., Ross, A. J. & Whittaker, J. E. The palaeoenvironment related to a partial Iguanodon skeleton from the Higher Weald Clay (Barremian, Early Cretaceous) at Smokejacks Brickworks (Ockley, Surrey, UK), primarily based on palynomorphs and ostracods. Cretac. Res. 29, 417–444 (2008).
Škaloud, P., Rindi, F., Boedeker, C. & Leliaert, F. Freshwater Flora of Central Europe, Vol 13: Chlorophyta: Ulvophyceae. pp. 288 (Springer Spektrum, 2018).
Darienko, T., Rad-Menéndez, C., Campbell, C. N. & Pröschold, T. Molecular phylogeny of unicellular marine coccoid inexperienced algae revealed new insights into the systematics of the Ulvophyceae (Chlorophyta). Microorganisms 9, 1586 (2021).
Comments
0 comments