Phylogenomics: the beginning of incongruence?

Jeffroy, Olivier; Brinkmann, Henner; Delsuc, Frédéric; Piégay, Hervé

doi:10.1016/j.tig.2006.02.003

Cited by 639 publications

(557 citation statements)

References 38 publications

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“…We also find that E. grandis has the largest number of genes in tandem repeats (12,570, 34% of the total) reported among sequenced plant genomes (Table 1 and Supplementary Information section 3). The low frequency of contig breaks separating tandem gene pairs (Extended Data Fig.…”

Section: Research Articlesupporting

confidence: 52%

“…3) and supports the grouping of Populus and Jatropha (order Malpighiales) with malvids rather than fabids, in agreement with other recent whole-genome studies 9,10 . The discrepancy between our genome-wide analyses and the angiosperm phylogeny group (APG) consensus highlights important methodological trade-offs between sampling more characters (as in our genome-wide study) versus more taxa (as per APG) 11,12 .…”

Section: Genome Evolution and Phylogenymentioning

confidence: 75%

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The genome of Eucalyptus grandis

Myburg¹,

Grattapaglia²,

Tuskan³

et al. 2014

Nature

761

750

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Eucalypts are the world's most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled .94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.A major opportunity for a sustainable energy and biomaterials economy in many parts of the world lies in a better understanding of the molecular basis of superior growth and adaptation in woody plants. Part of this opportunity involves species of Eucalyptus L'Hér, a genus of woody perennials native to Australia 1 . The remarkable adaptability of eucalypts coupled with their fast growth and superior wood properties has driven their rapid adoption for plantation forestry in more than 100 countries across six continents (.20 million ha) 2 , making eucalypts the most widely planted hardwood forest trees in the world. The subtropical E. grandis and the temperate E. globulus stand out as targets of breeding programmes worldwide. Planted eucalypts provide key renewable resources for the production of pulp, paper, biomaterials and bioenergy, while mitigating human pressures on native forests 3 . Eucalypts also have a large diversity and high concentration of essential oils (mixtures of mono-and sesquiterpenes), many of which have ecological functions as well as medicinal and industrial uses. Predominantly outcrossers 1 with hermaphroditic animal-pollinated flowers, eucalypts are highly heterozygous and display pre-and postzygotic barriers to selfing to reduce inbreeding depression for fitness and survival 4 .To mitigate the challenge of assembling a highly heterozygous genome, we sequenced the genome of 'BRASUZ1', a 17-year-old E. grandis genotype derived from one generation of selfing. The availability of annotated forest tree genomes from two separately evolving rosid lineages, Eucalyptus (order Myrtales) and Populus (order Malpighiales 5 ), in combination with genomes from domesticated woody plants (for example, Vitis, Prunus, Citrus), provides a comparative foundation for addressing

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Section: Research Articlesupporting

confidence: 52%

Section: Genome Evolution and Phylogenymentioning

confidence: 75%

The genome of Eucalyptus grandis

Myburg¹,

Grattapaglia²,

Tuskan³

et al. 2014

Nature

761

750

View full text Add to dashboard Cite

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“…When analyzing phylogenomic datasets, proper modeling of the amino acid substitution process is crucial because the use of overly simplistic models can lead to inaccurate phylogenetic inferences (reviewed in [13][14][15][16][17]. For example, the monophyly of Chordata was not confidently resolved from phylogenomic data until sophisticated substitution models were applied (18,19).…”

Section: Addressing Biases In Phylogenetic Reconstructionmentioning

confidence: 99%

Genomic data do not support comb jellies as the sister group to all other animals

Pisani

Pett

Dohrmann

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

300

336

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Understanding how complex traits, such as epithelia, nervous systems, muscles, or guts, originated depends on a well-supported hypothesis about the phylogenetic relationships among major animal lineages. Traditionally, sponges (Porifera) have been interpreted as the sister group to the remaining animals, a hypothesis consistent with the conventional view that the last common animal ancestor was relatively simple and more complex body plans arose later in evolution. However, this premise has recently been challenged by analyses of the genomes of comb jellies (Ctenophora), which, instead, found ctenophores as the sister group to the remaining animals (the "Ctenophora-sister" hypothesis). Because ctenophores are morphologically complex predators with true epithelia, nervous systems, muscles, and guts, this scenario implies these traits were either present in the last common ancestor of all animals and were lost secondarily in sponges and placozoans (Trichoplax) or, alternatively, evolved convergently in comb jellies. Here, we analyze representative datasets from recent studies supporting Ctenophora-sister, including genome-scale alignments of concatenated protein sequences, as well as a genomic gene content dataset. We found no support for Ctenophora-sister and conclude it is an artifact resulting from inadequate methodology, especially the use of simplistic evolutionary models and inappropriate choice of species to root the metazoan tree. Our results reinforce a traditional scenario for the evolution of complexity in animals, and indicate that inferences about the evolution of Metazoa based on the Ctenophora-sister hypothesis are not supported by the currently available data.Metazoa | Ctenophora | Porifera | phylogenomics | evolution R esolving the phylogenetic relationships close to the root of the animal tree of life, which encompass the phyla Porifera (sponges), Cnidaria (jellyfish, corals, and their allies), Ctenophora (comb jellies), Placozoa (the "plate animals" of the genus Trichoplax), and Bilateria (the group containing all remaining phyla), is fundamental to understanding early animal evolution and the emergence of complex traits [reviewed by Dohrmann and Wörheide (1)]. Traditionally, sponges have been recognized as the sister group to the remaining animals (the "Porifera-sister" hypothesis). Under this scenario, true epithelia (with belt desmosomes connecting neighboring cells) and extracellular digestion are conventionally thought to have been primitively absent in sponges, having evolved in the common ancestor of Placozoa, Ctenophora, Cnidaria, and Bilateria. Within this group, gap junctions between neighboring cells, ectodermal and endodermal germ layers, sensory cells, nerve cells, and muscle cells evolved only once in the common ancestor of Ctenophora, Cnidaria, and Bilateria. Thus, Porifera-sister is consistent with the view that the last common ancestor of the animals was relatively simple and more complex body plans evolved after sponges had separated from the other animal lineages. However, a s...

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“…The possible pitfalls associated with phylogenomic studies include systematic errors that can be traced back to some kind of model misspecifications (Philippe et al, 2005a) and caused mainly by heterogeneity of evolutionary rates among taxa Philippe et al, 2005b) and compositional bias (Blanquart and Lartillot, 2008;Jeffroy et al, 2006;Lartillot and Philippe, 2008;Phillips et al, 2004). Empirical protocols have been designed to detect and reduce the impact of systematic error in genome-scale studies (Rodríguez-Ezpeleta et al, 2007) but the ultimate solution lies in the development of improved models of sequence evolution (Felsenstein, 2004;Philippe et al, 2005a;Steel, 2005).…”

Section: Introductionmentioning

confidence: 99%

Additional molecular support for the new chordate phylogeny

Delsuc

Tsagkogeorga

Lartillot

et al. 2008

Genesis

219

178

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Summary: Recent phylogenomic analyses have suggested tunicates instead of cephalochordates as the closest living relatives of vertebrates. In direct contradiction with the long accepted view of Euchordates, this new phylogenetic hypothesis for chordate evolution has been the object of some skepticism. We assembled an expanded phylogenomic dataset focused on deuterostomes. Maximum-likelihood using standard models and Bayesian phylogenetic analyses using the CAT site-heterogeneous mixture model of amino-acid replacement both provided unequivocal support for the sister-group relationship between tunicates and vertebrates (Olfactores). Chordates were recovered as monophyletic with cephalochordates as the most basal lineage. These results were robust to both gene sampling and missing data. New analyses of ribosomal rRNA also recovered Olfactores when compositional bias was alleviated. Despite the inclusion of 25 taxa representing all major lineages, the monophyly of deuterostomes remained poorly supported. The implications of these phylogenetic results for interpreting chordate evolution are discussed in light of recent advances from evolutionary developmental biology and genomics. genesis 46:592-604, 2008. V V C 2008 Wiley-Liss, Inc.

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Phylogenomics: the beginning of incongruence?

Cited by 639 publications

References 38 publications

The genome of Eucalyptus grandis

The genome of Eucalyptus grandis

Genomic data do not support comb jellies as the sister group to all other animals

Additional molecular support for the new chordate phylogeny

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