Contrasting spatial genetic structure in Annona crassiflora populations from fragmented and pristine savannas

Collevatti, Rosane Garcia; Telles, Mariana P. C.; Lima, Jacqueline S.; Gouveia, Felipe Oliveira; Soares, Thannya Nascimento

doi:10.1007/s00606-014-0997-9

Cited by 18 publications

(12 citation statements)

References 47 publications

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“…We used 67% of sites for training and performed 200 bootstrap replicates, and the number of observed sites was calculated as the total length of the pseudoreference. We used an angiosperm‐wide mutation rate of 5.35 × 10 −9 sites/year (De la Torre, Li, Van De Peer, & Ingvarsson, 2017) and a generation time of 15 years based on the one proposed for the Annonaceae species Annona crassiflora (Collevatti, Telles, Lima, Gouveia, & Soares, 2014). In addition, sequencing error can skew the SFS by inflating the number of singletons, so we ran analyses using the entire SFS, and then reran with singletons removed to ensure similar histories were reached.…”

Section: Methodsmentioning

confidence: 99%

Phylogenomic approaches reveal how climate shapes patterns of genetic diversity in an African rain forest tree species

et al. 2020

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The world's second largest expanse of tropical rainforest is in Central Africa, and it harbours enormous species diversity. Population genetic studies have consistently revealed significant structure across Central African rainforest plants. In particular, previous studies have repeatedly demonstrated a north–south genetic discontinuity around the equatorial line, in a continuous expanse of rainforest where a climatic inversion is documented. Here, we took a phylogeographic approach by sequencing 351 nuclear markers in 112 individuals across the distribution of the African rainforest tree species Annickia affinis (Annonaceae). We showed for the first time that the north–south divide is the result of a single, major colonization event across the climatic inversion from an ancestral population located in Gabon. We suggested that differences in ecological niche of populations located on either side of this inversion may have contributed to this phylogenetic discontinuity. We found evidence for inland dispersal, predominantly in northern areas, and variable demographic histories among genetic clusters, indicating that populations responded differently to past climate change. We show how newly developed genomic tools can provide invaluable insights into our understanding of tropical rainforest evolutionary dynamics.

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Section: Methodsmentioning

confidence: 99%

Phylogenomic approaches reveal how climate shapes patterns of genetic diversity in an African rain forest tree species

et al. 2020

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“…312 scaffolds >100 kb were kept, totalling 646.64 Mb (98.46% of the total assembly). We assumed a generation time of 15 years (Collevatti et al, 2014) and a per-generation mutation rate of 7 × 10 −9 . PSMC was otherwise conducted using default parameters.…”

Section: Population Size Changes Inferencementioning

confidence: 99%

Chromosome‐level reference genome of the soursop (Annonamuricata): A new resource for Magnoliid research and tropical pomology

Strijk

Hinsinger

Roeder

et al. 2021

Molecular Ecology Resources

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“…Mb (98.46 percent of the total assembly). We assume a generation time of 15 years (Collevatti et al 2014) and a per-generation mutation rate of 7x10-9. PSMC was otherwise conducted using default parameters.…”

Section: Population Size Changes Inferencementioning

confidence: 99%

The soursop genome and comparative genomics of basal angiosperms provide new insights on evolutionary incongruence

Strijk¹,

Hinsinger²,

Mm³

et al. 2019

Preprint

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Deep relationships and the sequence of divergence among major lineages of angiosperms (magnoliids, monocots and eudicots) remain ambiguous and differ depending on analytical approaches and datasets used.Complete genomes potentially provide opportunities to resolve these uncertainties, but two recently published magnoliid genomes instead deliver further conflicting signals. To disentangle key angiosperm relationships, we report a high-quality draft genome for the soursop (Annona muricata, Annonaceae). We reconstructed phylogenomic trees and show that the soursop represents a genomic mosaic supporting different histories, with scaffolds almost exclusively supporting single topologies. However, coalescent methods and a majority of genes support magnoliids as sister to monocots and eudicots, where previous whole genome-based studies remained inconclusive. This result is clear and consistent with recent studies using plastomes. The soursop genome highlights the need for more early diverging angiosperm genomes and critical assessment of the suitability of such genomes for inferring evolutionary history. 36 37 38 39 40 41 42 43 44 45 46 47 2 successive reductions in the number of whorls of both the perianth and the androecium. In both cases, disparate reductions may have paved the way for the evolution of clade specific features of genomes and flower morphology in contemporary clades. Since the publication of the first plant genome, that of Arabidopsis thaliana (Initiative 2000), there has been a steady increase in the number of sequenced eudicot and monocot genomes. However, with the exception of the iconic Amborella trichopoda, basal angiosperm diversity represented by the ancient lineages of Nymphaeales, Austrobaileyales, Chloranthales, and magnoliids has largely been overlooked. After eudicots and monocots, Magnoliidae are the most diverse clade of angiosperms (Massoni et al. 2014) with 9,000-10,000 species in four orders (Canellales, Piperales, Laurales and Magnoliales). However, despite this diversity and economic value (e.g. avocado, black pepper, cinnamon, soursop), only two genomes have been

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Contrasting spatial genetic structure in Annona crassiflora populations from fragmented and pristine savannas

Cited by 18 publications

References 47 publications

Phylogenomic approaches reveal how climate shapes patterns of genetic diversity in an African rain forest tree species

Phylogenomic approaches reveal how climate shapes patterns of genetic diversity in an African rain forest tree species

Chromosome‐level reference genome of the soursop (Annonamuricata): A new resource for Magnoliid research and tropical pomology

The soursop genome and comparative genomics of basal angiosperms provide new insights on evolutionary incongruence

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