The potential of genome-wide RAD sequences for resolving rapid radiations: a case study in Cactaceae

Bombonato, Juliana Rodrigues; Amaral, Danilo T.; Silva, Gislaine Angélica Rodrigues; Khan, Gulzar; Moraes, Evandro M.; Andrade, Sónia C. S.; Eaton, Deren A. R.; Alonso, Diego Peres; Ribolla, Paulo Eduardo Martins; Taylor, Nigel; Zappi, Daniela; Franco, Fernando Faria

doi:10.1016/j.ympev.2020.106896

Cited by 22 publications

(28 citation statements)

References 51 publications

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“…The analyses performed agree with the general phylogenetic conclusions of Bombonato et al (2020) recovering the genus as monophyletic with species allocated in at least five main clades, with well‐supported branches (Figure S1). Also, Cereus fernambucensis subsp.…”

Section: Resultssupporting

confidence: 86%

“…We re‐analyzed the ddRAD (Double digest restriction‐site associated DNA) dataset generated by our group (Bombonato et al, 2020). To improve computational processing, we used a subset of the samples represented by one individual per species/population (details in Table S1).…”

Section: Methodsmentioning

confidence: 99%

“…A recent phylogenomic (ddRAD‐seq; Bombonato et al, 2020) study of Cereus has supported the monophyly of the genus and identified at least four distinct lineages with mostly discrete geographical distributions associated with the DD. However, biogeographical reconstructions have only been applied to the relatively poorly resolved plastid phylogeny ( trnS ‐ trnG region) and, according to these reconstructions, Cereus originated in the Cerrado domain during the Plio‐Pleistocene transition (Franco, Jojima, et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

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Tracking the xeric biomes of South America: The spatiotemporal diversification of Mandacaru cactus

Amaral

Minhós-Yano

Oliveira

et al. 2021

Journal of Biogeography

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Aim The interconnectedness and biotic interchange among Neotropical biomes are thought to play an important role in driving adaptation and diversification. However, how these processes are in synteny to trait evolution in species of open and xeric areas is poorly studied. Here, we investigate the spatial and temporal dimensions of evolution and candidate traits associated with biome shifts in xeric vegetation, focusing on the family Cactaceae. Location Xeric and open areas of South America. Taxon Genus Cereus Mill. (Cactaceae, Cereeae). Methods We applied biogeographical reconstructions on a time‐calibrated phylogeny inferred from multilocus data (ddRAD‐Seq) using Bayesian analyses on BEAST2, species distribution modelling in Maxent, the reconstruction of biome affinities and niche shift analyses based on abiotic traits (climate and soil) using Mk‐model in BioGeoBEARS, and phenotypic trait‐based analysis in Mesquite. Results The Cerrado domain is the ancestral area of Cereus, with most diversification events occurring in a time of intense orogenesis, climatic changes, and marine regressions within the last 5 Mya. Events of biome transition from the seasonally dry tropical forest (SDTF) were also associated with trait and niche shifts. Main conclusions The diversification of the xerophyte genus Cereus is associated with the climatic and geomorphological instabilities of the Pliocene and Pleistocene epochs. The Cerrado domain states an important region of dispersal for the genus. Some geographical range movements involved biome shifts associated with niche evolution while others were restricted to a simple biogeographical transition without niche change. Particular clades that experienced biome shifts displayed some phenotypic state changes, suggesting a role of biotic traits for environment transition. The results observed in Cereus may be a biogeographical pattern that should be tested with other cactus species, such as Pilosocereus spp., or species of xeric habitats, such as Annonaceae and Vochysiaceae.

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Section: Resultssupporting

confidence: 86%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Tracking the xeric biomes of South America: The spatiotemporal diversification of Mandacaru cactus

Amaral

Minhós-Yano

Oliveira

et al. 2021

Journal of Biogeography

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“…To solve this problem, Tonini et al (2015) reported that coalescent methods could perform well as a supermatrix [71]. Moreover, for the rapid diversification and ancient radiation of plants, the concatenation approach is preferred over other methods [72]. According to this study, the BI-tree obtained in BEAST showed well-supported evidence compared with that obtained with other methods (e.g., MP tree and ML tree) using the concatenated datasets.…”

Section: The Genomic Data For Inferring the Phylogeny Of Curcumamentioning

confidence: 61%

Incompatibility Phylogenetic Signals between Double-Digest Restriction Site-Associated DNA Sequencing and Plastid Genomes in Chinese Curcuma (Zingiberaceae)—A Recent Qinghai–Tibetan Plateau Diversification Genera

Liang

Deng

Gao

et al. 2022

Forests

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Curcuma is of high economic value, credited to its medicinal, edible, and ornamental properties, which possess all signatures of adaptability, and rapid radiation, especially species of Curcuma (Chinese Curcuma, a recent Qinghai–Tibetan Plateau diversification genera) scattered in China. However, little is known about the incongruent phylogenetic signals within this genera from different inheritance patterns that will militate against the further development of this genera. In this research, we applied complete chloroplast genome data together with double-digest restriction site-associated DNA sequencing data (ddRAD-seq) strategy to investigate phylogenetic signals of Chinese Curcuma species, clustering using two RAD analysis pipelines (STACKS and pyRAD). Phylogenetic trees were obtained from each locus based on the maximum likelihood (ML) and multispecies coalescent (BEAST) methods. For visual comparison, multi-method and different datasets were used to infer the phylogeny. We discovered inconsistent relationships for the Chinese Curcuma with varying degrees of support using different methods and datasets.

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“…Although relatively few genomic-scale studies were recovered in our literature survey, we noticed an increasing use of genome-wide markers in the past five years ( Figure 1 b). For example, different methods to sequence a reduced representation of genomes have been used in evolutionary studies on cacti, resolving rapid and recent diversification in this group (e.g., [ 50 , 62 , 63 ]). In addition, de novo assembled genomes, transcriptomes, and plastomes have been successfully used in some cacti groups (e.g., [ 32 ]).…”

Section: Discussionmentioning

confidence: 99%

Evolutionary Genetics of Cacti: Research Biases, Advances and Prospects

Franco

Amaral

Bonatelli

et al. 2022

Genes

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Here, we present a review of the studies of evolutionary genetics (phylogenetics, population genetics, and phylogeography) using genetic data as well as genome scale assemblies in Cactaceae (Caryophyllales, Angiosperms), a major lineage of succulent plants with astonishing diversity on the American continent. To this end, we performed a literature survey (1992–2021) to obtain detailed information regarding key aspects of studies investigating cactus evolution. Specifically, we summarize the advances in the following aspects: molecular markers, species delimitation, phylogenetics, hybridization, biogeography, and genome assemblies. In brief, we observed substantial growth in the studies conducted with molecular markers in the past two decades. However, we found biases in taxonomic/geographic sampling and the use of traditional markers and statistical approaches. We discuss some methodological and social challenges for engaging the cactus community in genomic research. We also stressed the importance of integrative approaches, coalescent methods, and international collaboration to advance the understanding of cactus evolution.

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The potential of genome-wide RAD sequences for resolving rapid radiations: a case study in Cactaceae

Cited by 22 publications

References 51 publications

Tracking the xeric biomes of South America: The spatiotemporal diversification of Mandacaru cactus

Tracking the xeric biomes of South America: The spatiotemporal diversification of Mandacaru cactus

Incompatibility Phylogenetic Signals between Double-Digest Restriction Site-Associated DNA Sequencing and Plastid Genomes in Chinese Curcuma (Zingiberaceae)—A Recent Qinghai–Tibetan Plateau Diversification Genera

Evolutionary Genetics of Cacti: Research Biases, Advances and Prospects

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