Historical biogeography of Vochysiaceae reveals an unexpected perspective of plant evolution in the Neotropics

Gonçalves, Deise Josely Pereira; Shimizu, Gustavo Hiroaki; Ortiz, Edgardo M.; Jansen, Robert K.; Simpson, Beryl B.

doi:10.1002/ajb2.1502

Cited by 16 publications

(17 citation statements)

References 76 publications

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“…In the ML analysis, Vochysieae are monophyletic, but the support is low; in the ASTRAL analysis the clade Vochysia + Salvertia is sister to Erisma , with moderate support. Salvertia was retrieved as sister to Vochysia , corroborating some previous studies (Sytsma et al, 2004; Gonçalves et al, 2019, 2020). The placement of Salvertia has always been intriguing in the history of the family.…”

Section: Discussionsupporting

confidence: 89%

“…While most species of Vochysiaceae have flowers with one or three petals and are pollinated by bees, Salvertia bears five‐petaled, completely white flowers, associated with hawkmoth pollination (Oliveira et al, 2004). Callisthene appears sister to a clade formed by Qualea , with Ruizterania embedded in it, corroborating a placement highly supported in Gonçalves et al, 2020). Further studies using more molecular markers and increasing the number of species of Erisma , Callisthene , Qualea (including species assigned to Ruizterania ), and Vochysia are necessary before taxonomic decisions are reached.…”

Section: Discussionsupporting

confidence: 74%

“…The relationships recovered in the ML analysis appear congruent with plastome phylogenetic studies, despite relatively low support for the monophyly of Vochysieae. Our ASTRAL topology does not correspond to the plastome phylogeny of Gonçalves et al (2020), since we retrieve Erisma as sister to Vochysia + Salvertia instead.…”

Section: Vochysiaceaementioning

confidence: 91%

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A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set

Maurin

Anest

Bellot

et al. 2021

American J of Botany

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To further advance the understanding of the species-rich, economically and ecologically important angiosperm order Myrtales in the rosid clade, comprising nine families, approximately 400 genera and almost 14,000 species occurring on all continents (except Antarctica), we tested the Angiosperms353 probe kit. METHODS:We combined high-throughput sequencing and target enrichment with the Angiosperms353 probe kit to evaluate a sample of 485 species across 305 genera (76% of all genera in the order). RESULTS:Results provide the most comprehensive phylogenetic hypothesis for the order to date. Relationships at all ranks, such as the relationship of the early-diverging families, often reflect previous studies, but gene conflict is evident, and relationships previously found to be uncertain often remain so. Technical considerations for processing HTS data are also discussed.CONCLUSIONS: High-throughput sequencing and the Angiosperms353 probe kit are powerful tools for phylogenomic analysis, but better understanding of the genetic data available is required to identify genes and gene trees that account for likely incomplete lineage sorting and/or hybridization events.

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Section: Discussionsupporting

confidence: 89%

Section: Discussionsupporting

confidence: 74%

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A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set

Maurin

Anest

Bellot

et al. 2021

American J of Botany

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“…6 ) presented here is in close proximity to previously reported dates (104.90 Ma compared to 111 Ma, Sytsma et al [ 28 ]; 116.4 Ma, Berger et al [ 2 ]; 90.7 Ma, Thornhill et al [ 53 ]). However, Gonçalves et al [ 54 ] using 78 protein coding genes from 122 chloroplast genomes of Myrtales, combined with four Myrtales fossil sites and a secondary calibration point, estimated the divergence time of Myrtales to be 125.5 Ma (95% HPD = 130.9–120.3 Ma) during the upper Cretaceous. Fossil limitations, different methods, size of molecular data and taxonomic sampling cannot be perfectly compared across all studies, with changes leading to differences in age estimates.…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of chloroplast genome structure and molecular dating in Myrtales

et al. 2021

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Background Myrtales is a species rich branch of Rosidae, with many species having important economic, medicinal, and ornamental value. At present, although there are reports on the chloroplast structure of Myrtales, a comprehensive analysis of the chloroplast structure of Myrtales is lacking. Phylogenetic and divergence time estimates of Myrtales are mostly constructed by using chloroplast gene fragments, and the support for relationships is low. A more reliable method to reconstruct the species divergence time and phylogenetic relationships is by using whole chloroplast genomes. In this study, we comprehensively analyzed the structural characteristics of Myrtales chloroplasts, compared variation hotspots, and reconstructed the species differentiation time of Myrtales with four fossils and one secondary calibration point. Results A total of 92 chloroplast sequences of Myrtales, representing six families, 16 subfamilies and 78 genera, were obtained including nine newly sequenced chloroplasts by whole genome sequencing. Structural analyses showed that the chloroplasts range in size between 152,214–171,315 bp and exhibit a typical four part structure. The IR region is between 23,901–36,747 bp, with the large single copy region spanning 83,691–91,249 bp and the small single copy region spanning 11,150–19,703 bp. In total, 123–133 genes are present in the chloroplasts including 77–81 protein coding genes, four rRNA genes and 30–31 tRNA genes. The GC content was 36.9–38.9%, with the average GC content being 37%. The GC content in the LSC, SSC and IR regions was 34.7–37.3%, 30.6–36.8% and 39.7–43.5%, respectively. By analyzing nucleotide polymorphism of the chloroplast, we propose 21 hypervariable regions as potential DNA barcode regions for Myrtales. Phylogenetic analyses showed that Myrtales and its corresponding families are monophyletic, with Combretaceae and the clade of Onagraceae + Lythraceae (BS = 100%, PP = 1) being sister groups. The results of molecular dating showed that the crown of Myrtales was most likely to be 104.90 Ma (95% HPD = 87.88–114.18 Ma), and differentiated from the Geraniales around 111.59 Ma (95% HPD = 95.50–118.62 Ma). Conclusions The chloroplast genome structure of Myrtales is similar to other angiosperms and has a typical four part structure. Due to the expansion and contraction of the IR region, the chloroplast genome sizes in this group are slightly different. The variation of noncoding regions of the chloroplast genome is larger than those of coding regions. Phylogenetic analysis showed that Combretaceae and Onagraceae + Lythraceae were well supported as sister groups. Molecular dating indicates that the Myrtales crown most likely originated during the Albian age of the Lower Cretaceous. These chloroplast genomes contribute to the study of genetic diversity and species evolution of Myrtales, while providing useful information for taxonomic and phylogenetic studies of Myrtales.

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“…Dispersal events from forest to open habitats is one of the main factors explaining richness in Neotropical biodiversity [ 16 ]. Even though in Stigmaphyllon, those dispersal events occurred mostly among forested biomes, its single Cerrado lineage seems to point to an older diversification of this biome, such as in those from Vochysiaceae (20.0–15.0 Mya) [ 51 ]. Few species of Stigmaphyllon successfully colonized the Cerrado biome, such as S. jobertii , S. occidentale , S. tomentosum, and S. urenifolium .…”

Section: Discussionmentioning

confidence: 99%

Biogeography of Stigmaphyllon (Malpighiaceae) and a Meta-Analysis of Vascular Plant Lineages Diversified in the Brazilian Atlantic Rainforests Point to the Late Eocene Origins of This Megadiverse Biome

Almeida

Berg

2020

Plants

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We investigated the biogeography of Stigmaphyllon, the second-largest lianescent genus of Malpighiaceae, as a model genus to reconstruct the age and biogeographic history of the Brazilian Atlantic Rainforest (BAF). Few studies to date have focused on the tertiary diversification of plant lineages in the BAFs, especially on Stigmaphyllon. Phylogenetic relationships for 24 species of Stigmaphyllon (18 ssp. From the Atlantic forest (out of 31 spp.), three spp. from the Amazon Rainforest, two spp. from the Caatinga biome, and a single species from the Cerrado biome) were inferred based on one nuclear DNA (PHYC) and two ribosomal DNA (ETS, ITS) regions using parsimony and Bayesian methods. A time-calibrated phylogenetic tree for ancestral area reconstructions was additionally generated, coupled with a meta-analysis of vascular plant lineages diversified in the BAFs. Our results show that: (1) Stigmaphyllon is monophyletic, but its subgenera are paraphyletic; (2) the most recent common ancestor of Stigmaphyllon originated in the Brazilian Atlantic Rainforest/Caatinga region in Northeastern Brazil ca. 26.0 Mya; (3) the genus colonized the Amazon Rainforest at two different times (ca. 22.0 and 6.0 Mya), the Caatinga biome at least four other times (ca. 14.0, 9.0, 7.0, and 1.0 Mya), the Cerrado biome a single time (ca. 15.0 Mya), and the Southern Atlantic Rainforests five times (from 26.0 to 9.0 Mya); (4) a history of at least seven expansion events connecting the Brazilian Atlantic Rainforest to other biomes from 26.0 to 9.0 Mya, and (5) a single dispersion event from South America to Southeastern Asia and Oceania at 22.0 Mya via Antarctica was proposed. Compared to a meta-analysis of time-calibrated phylogenies for 64 lineages of vascular plants diversified in the Brazilian Atlantic Rainforests, our results point to a late Eocene origin for this megadiverse biome.

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Historical biogeography of Vochysiaceae reveals an unexpected perspective of plant evolution in the Neotropics

Abstract: This is the author manuscript accepted for publication and has undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as

Cited by 16 publications

References 76 publications

A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set

A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set

Comparative analysis of chloroplast genome structure and molecular dating in Myrtales

Biogeography of Stigmaphyllon (Malpighiaceae) and a Meta-Analysis of Vascular Plant Lineages Diversified in the Brazilian Atlantic Rainforests Point to the Late Eocene Origins of This Megadiverse Biome

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