Phylogenomics of the major tropical plant family Annonaceae using targeted enrichment of nuclear genes

Couvreur, Thomas L. P.; Helmstetter, Andrew J.; Koenen, Erik E.; Bethume, Kevin; Brandão, Rita D.; Little, Stefan A.; Sauquet, Hervé; Erkens, Roy

doi:10.1101/440925

Cited by 4 publications

(2 citation statements)

References 81 publications

(105 reference statements)

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“…We are grateful to Etienne Delannoy who coordinated the sequencing of the Marsypopetalum transcriptome. This manuscript is also available as a pre-print on BioRXiv (Couvreur et al, 2018).…”

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confidence: 99%

Phylogenomics of the Major Tropical Plant Family Annonaceae Using Targeted Enrichment of Nuclear Genes

et al. 2019

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Targeted enrichment and sequencing of hundreds of nuclear loci for phylogenetic reconstruction is becoming an important tool for plant systematics and evolution. Annonaceae is a major pantropical plant family with 110 genera and ca. 2,450 species, occurring across all major and minor tropical forests of the world. Baits were designed by sequencing the transcriptomes of five species from two of the largest Annonaceae subfamilies. Orthologous loci were identified. The resulting baiting kit was used to reconstruct phylogenetic relationships at two different levels using concatenated and gene tree approaches: a family wide Annonaceae analysis sampling 65 genera and a species level analysis of tribe Piptostigmateae sampling 29 species with multiple individuals per species. DNA extraction was undertaken mainly on silicagel dried leaves, with two samples from herbarium dried leaves. Our kit targets 469 exons (364,653 bp of sequence data), successfully capturing sequences from across Annonaceae. Silicagel dried and herbarium DNA worked equally well. We present for the first time a nuclear gene-based phylogenetic tree at the generic level based on 317 supercontigs. Results mainly confirm previous chloroplast based studies. However, several new relationships are found and discussed. We show significant differences in branch lengths between the two large subfamilies Annonoideae and Malmeoideae. A new tribe, Annickieae, is erected containing a single African genus Annickia. We also reconstructed a well-resolved species-level phylogenetic tree of the Piptostigmteae tribe. Our baiting kit is useful for reconstructing well-supported phylogenetic relationships within Annonaceae at different taxonomic levels. The nuclear genome is mainly concordant with plastome information with a few exceptions. Moreover, we find that substitution rate heterogeneity between the two subfamilies is also found within the nuclear compartment, and not just plastomes and ribosomal DNA as previously shown. Our results have implications for understanding the biogeography, molecular dating and evolution of Annonaceae.

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“…We are grateful to Etienne Delannoy who coordinated the sequencing of the Marsypopetalum transcriptome. This manuscript is also available as a pre-print on BioRXiv (Couvreur et al, 2018).…”

mentioning

confidence: 99%

Phylogenomics of the Major Tropical Plant Family Annonaceae Using Targeted Enrichment of Nuclear Genes

et al. 2019

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“…Approaches that can target multiple independent nuclear coded markers (e.g. hybrid capture techniques) may be more fruitful and the development of protocols for such markers is of importance to further address problems in species-level analyses in Annonaceae (Couvreur et al 2018). …”

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A taxonomic revision of the Neotropical genus Cremastosperma (Annonaceae), including five new species

Pirie¹,

Chatrou²,

Maas³

2018

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We present a taxonomic revision of Cremastosperma, a genus of Neotropical Annonaceae occurring in lowland to premontane wet forest, mostly in areas surrounding the Andean mountain chain. We recognise 34 species, describing five as new here: from east of the Andes, C.brachypodum Pirie & Chatrou, sp. nov. and C.dolichopodum Pirie & Maas, sp. nov., endemic to Peru; C.confusum Pirie, sp. nov., from southern Peru and adjacent Bolivia and Brazil; and C.alticola Pirie & Chatrou, sp. nov., at higher elevations in northern Peru and Ecuador; and from west of the Andes, C.osicola Pirie & Chatrou, sp. nov. endemic to Costa Rica, the most northerly distributed species of the genus. We provide an identification key, document diagnostic characters and distributions and provide illustrations and extensive lists of specimens, also presenting the latter in the form of mapping data with embedded links to images available online. Of the 34 species, 22 are regional endemics. On the basis of the extent of occurrence and area of occupancy of species estimated from the distribution data, we designate IUCN threat categries for all species. Fourteen species proved to be endangered (EN) and a further one critically endangered (CR), reflecting their rarity and narrow known distributions.

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Long-distance dispersal shaped the diversity of tribe Dorstenieae (Moraceae)

Zhang

Gardner

Zerega

et al. 2019

Preprint

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1 Aim: The Neotropics have the highest terrestrial biodiversity on earth. Investigating the 2 relationships between the floras of the Neotropics and other tropical areas is critical to 3 understanding the origin and evolution of this mega-diverse region. Tribe Dorstenieae (Moraceae) 4 has a pantropical distribution and almost equal number of species on both sides of the Atlantic.5In this study, we investigate the relationship between the African and Neotropical floras using 6 Dorstenieae (15 genera, 156 species, Moraceae) as a model clade. 7 Location: the Neotropics and Africa. 8 Methods: We used a targeted enrichment strategy with herbarium samples and a nuclear bait set 9 to assemble a data set of 102 genes sampled from 83 (53%) species and fifteen genera (100%) of 10 Dorstenieae, and five outgroup species. Phylogenetic relationships were reconstructed with 11 maximum likelihood and coalescent approaches. This phylogeny was dated with a Bayesian 12 relaxed clock model and four fossil calibrations. The biogeographic history of the group was 13 then reconstructed with several dispersal-extinction-cladogenesis models (incl. DEC and DEC+J).14 Results: The crown-group ages of Dorstenieae and Dorstenia were estimated in the Cretaceous 15 (65.8-79.8 Ma) and the Paleocene (50.8-67.3 Ma), respectively. Tribe Dorstenieae as a whole 16 appears to have originated in the joint area of continental Africa, Madagascar and Asia-Oceania 17 area. The Neotropical species of Dorstenia diversified in the Eocene (29.8-44.7 Ma) and formed a 18 clade nested within the African lineages in the genus. Brosimum s.l., with a crown-group age at 19 the period of the Oligocene and Miocene (14.9-31.1 Ma), represents another Neotropical clade in 20 Dorstenieae. Main conclusions: Tribe Dorstenieae originated in the joint area of continental Africa, 1 Madagascar and Asia-Oceania area in the Cretaceous and then dispersed into Neotropics twice. 2 Neotropical diversification after long-distance dispersal across the Atlantic is the most plausible 3 explanation for the extant distribution pattern of Dorstenieae.4 5

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Phylogenomics of the major tropical plant family Annonaceae using targeted enrichment of nuclear genes

Cited by 4 publications

References 81 publications

Phylogenomics of the Major Tropical Plant Family Annonaceae Using Targeted Enrichment of Nuclear Genes

Phylogenomics of the Major Tropical Plant Family Annonaceae Using Targeted Enrichment of Nuclear Genes

A taxonomic revision of the Neotropical genus Cremastosperma (Annonaceae), including five new species

Long-distance dispersal shaped the diversity of tribe Dorstenieae (Moraceae)

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