Combining high-throughput sequencing and targeted loci data to infer the phylogeny of the “Adenocalymma-Neojobertia” clade (Bignonieae, Bignoniaceae)

Fonseca, Luiz Henrique M.; Lohmann, Lúcia G.

doi:10.1016/j.ympev.2018.01.023

Cited by 32 publications

(28 citation statements)

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“…The effects of the abovementioned sources of systematic error have generally been evaluated at high taxonomic levels, genus and above, in green plants (e.g., Ruhfel et al, 2014). Many plastid phylogenomic studies typically analyze plastome data as a single partition, or divided by a region (e.g., LSC, SSC, IR), using a concatenate "supergene" approach under maximum likelihood or Bayesian statistical methods (e.g., Fonseca & Lohmann, 2018). By adopting such limited methodological approach, these studies ignore potential conflict in inferred phylogenetic relationships among different genes or DNA stretches of the plastid genome.…”

Section: Introductionmentioning

confidence: 99%

Evaluating character partitioning and molecular models in plastid phylogenomics at low taxonomic levels: A case study using Amphilophium (Bignonieae, Bignoniaceae)

Thode

Lohmann

Sanmartín

2020

J of Sytematics Evolution

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The accurate analyses of massive amounts of data obtained through next-generation sequencing depend on the selection of appropriate evolutionary models. Many plastid phylogenomic studies typically analyze plastome data as a single partition, or divided by a region, using a concatenate "supergene" approach. The effects of molecular evolutionary models and character partition strategies on plastome-based phylogenies have generally been evaluated at higher taxonomic levels in green plants. Using plastome data from 32 species of Amphilophium, a genus of Neotropical lianas, we explored potential sources of topological incongruence with different plastid genome datasets and approaches. Specifically, we evaluated the effects of compositional heterogeneity, codon usage bias, positive selection, and incomplete lineage sorting as sources of systematic error (i.e., the recovery of well-supported conflicting topologies). We compared different datasets (e.g., non-coding regions, exons, and codon-aligned and translated amino acids) using concatenated approaches under siteheterogeneous and site-homogeneous models, as well as multispecies coalescent (MSC) methods. We found incongruences in recovered phylogenetic relationships, which were mainly located in short internodes. The MSC and concatenated approaches recovered similar topologies. The analysis of GC content and codon usage bias indicated higher substitution rates and AT excess at the third codon positions, and we found evidence of positive selection in 3% of amino acid sites. There were no significant differences among species in site biochemical profiles. We argue that the selection of appropriate partition strategies and evolutionary models is important to increase accuracy in phylogenetic relationships, even when using plastome datasets, which is still the primarily used genome in plant phylogenetics.

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Section: Introductionmentioning

confidence: 99%

Evaluating character partitioning and molecular models in plastid phylogenomics at low taxonomic levels: A case study using Amphilophium (Bignonieae, Bignoniaceae)

Thode

Lohmann

Sanmartín

2020

J of Sytematics Evolution

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“…The result of the AU test also demonstrated the non-monophyly of the Fargesia grossa clade and the Fargesia macclureana clade. The use of whole plastid genome sequences has the potential to increase the resolution of phylogenetic analyses at low taxonomic levels or among recently diverged species (Njuguna et al, 2013; Williams et al, 2016; Sancho et al, 2017; Uribe-Convers et al, 2017; Fonseca and Lohmann, 2018). Taxon sampling (including ingroups and outgroups) is important for phylogenetic inference, particularly for the complex temperate woody bamboos.…”

Section: Discussionmentioning

confidence: 99%

“…Thus, a high-quality phylogeny, including more representative taxa and a large number of genetic markers, is necessary to understand the evolutionary history of Fargesia . Full plastome sequencing has been shown to be useful in resolving complex evolutionary relationships in closely related species (Njuguna et al, 2013; Williams et al, 2016; Uribe-Convers et al, 2017; Fonseca and Lohmann, 2018). Despite the existence of previous phylogenetic analyses based on the plastomes of Arundinarieae (Ma et al, 2014; Attigala et al, 2016; Saarela et al, 2018), the phylogenetic relationships among Fargesia species are still poorly resolved.…”

Section: Introductionmentioning

confidence: 99%

Straight From the Plastome: Molecular Phylogeny and Morphological Evolution of Fargesia (Bambusoideae: Poaceae)

et al. 2019

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Fargesia is ecologically and economically important in mountainous forests. Many Fargesia species are also important sources of food for some endangered animals such as the giant panda. Recent molecular phylogenetic analyses have revealed Fargesia as a polyphyletic group despite some unclear lineage affinities. In the present study, we reconstructed the phylogeny of Fargesia and its allies, including Thamnocalamus, Arundinaria (incl. Bashania ), Yushania, Indocalamus, Ampelocalamus and Phyllostachys , from a plastome sequence matrix that contained 20 Fargesia and five Yushania species as ingroups, 16 species from nine other bamboo genera plus Oryza sativa and Zea mays as outgroups. Fargesia and its allies were broken into eight clades. Several Fargesia species were clustered into the Thamnocalamus clade and the Drepanostachyum + Himalayacalamus clade that rendered the polyphyly of Fargesia . The remaining six clades, including the Fargesia spathe clade, the Phyllostachys clade, Arundinaria fargesii , the Ampelocalamus clade, the Fargesia grossa clade, and the Fargesia macclureana clade, were identified. Molecular phylogenetic analyses supported that Yushania should be included in Fargesia (s.l.) which had synapomorphy of expanded leaf sheaths in varying degree at the basis of inflorescences, and further divided into the Fargesia spathe clade, the Fargesia grossa clade, and the Fargesia macclureana clade. All sampled species of Yushania were nested within the Fargesia grossa clade. The probable model of the origin of the species in the Fargesia spathe clade with spathe-like leaf sheath syndrome was proposed. Moreover, the formation of the spathe-like leaf sheath syndrome may be correlated with cold climatic conditions in Quaternary. Our results provide new sight into the phylogenetic relationship within Fargesia .

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“…Genome skimming via shotgun sequencing of total genomic DNA at relatively low coverage is an efficient approach to recover entire plastomes and nrDNA [47]. Recently, genome skimming has been widely employed to reconstruct the evolutionary relationship at lower taxonomic levels and among closely related species [51][52][53][54][55], as well as to investigate reticulate evolution in diverse plant clades [52,[56][57][58]. In this study, we generated plastome and nrDNA sequences from all currently recognized Paris species using genome skimming method.…”

Section: Introductionmentioning

confidence: 99%

Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)

Yang

Chase

et al. 2019

Preprint

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Background: Paris (Melanthiaceae) is an economically important but taxonomically difficult genus, which is unique in angiosperms because some species have extremely large nuclear genomes. Phylogenetic relationships within Paris have long been controversial. Based on complete plastomes and nuclear ribosomal DNA (nrDNA) sequences, this study aims to reconstruct a robust phylogenetic tree and explore historical biogeography and clade diversification in the genus.Results: All 29 species currently recognized in Paris were sampled. Whole plastomes and nrDNA sequences were generated by the genome skimming approach. Phylogenetic relationships were reconstructed using the maximum likelihood and Bayesian inference methods. Based on the phylogenetic framework and molecular dating, biogeographic scenarios and historical diversification of Paris were explored. Significant conflicts between plastid and nuclear datasets were identified, and the plastome tree is highly congruent with past interpretations of the morphology. Ancestral area reconstruction indicated that Paris may have originated in northeastern Asia and northern China, and has experienced multiple dispersal and vicariance events during its diversification. The rate of clade diversification has sharply accelerated since the Miocene/Pliocene boundary.Conclusions: Our results provide important insights for clarifying some of the long-standing taxonomic debates in Paris. Cytonuclear discordance may have been caused by ancient and recent hybridizations in the genus. The climatic and geological changes since the late Miocene, such as the intensification of Asian monsoon and the rapid uplift of Qinghai-Tibet Plateau, as well as the climatic fluctuations during the Pleistocene, played essential roles in driving range expansion and radiative diversification in Paris. Our findings challenge the theoretical prediction that large genome sizes may limit speciation.

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Combining high-throughput sequencing and targeted loci data to infer the phylogeny of the “Adenocalymma-Neojobertia” clade (Bignonieae, Bignoniaceae)

Cited by 32 publications

References 72 publications

Evaluating character partitioning and molecular models in plastid phylogenomics at low taxonomic levels: A case study using Amphilophium (Bignonieae, Bignoniaceae)

Evaluating character partitioning and molecular models in plastid phylogenomics at low taxonomic levels: A case study using Amphilophium (Bignonieae, Bignoniaceae)

Straight From the Plastome: Molecular Phylogeny and Morphological Evolution of Fargesia (Bambusoideae: Poaceae)

Plastome phylogenomics, biogeography, and clade diversification of Paris (Melanthiaceae)

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