Phylogeny, historical biogeography, and diversification of angiosperm order Ericales suggest ancient Neotropical and East Asian connections

Rose, Jeff; Kleist, Thomas; Löfstrand, Stefan; Drew, Bryan T.; Schönenberger, Jürg; Sytsma, Kenneth J.

doi:10.1016/j.ympev.2018.01.014

Cited by 103 publications

(125 citation statements)

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“…LDD has often been invoked to explain widely disjunct ranges in Carex and Cyperaceae as a whole (e.g., Escudero et al, ; Viljoen et al, ; Gebauer et al, ; Spalink et al, ; Míguez et al, ; Villaverde et al, ). A skewed distribution of dispersal events towards present times has also been observed in other groups in which LDD is regarded as a critical process shaping their biogeographic patterns (Tripp & McDade, ; Dupin et al, ; Ruhfel et al, ; Rose et al, ; Huang et al, ). With respect to the dispersal source, recurrent dispersal from E Asia is inferred not to have started until the late Oligocene‐early Miocene (c. 25–20 Mya; Figs.…”

Section: Discussionsupporting

confidence: 55%

A tale of worldwide success: Behind the scenes of Carex (Cyperaceae) biogeography and diversification

Martín‐Bravo

Jiménez‐Mejías

Villaverde

et al. 2019

J of Sytematics Evolution

168

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The megadiverse genus Carex (c. 2000 species, Cyperaceae) has a nearly cosmopolitan distribution, displaying an inverted latitudinal richness gradient with higher species diversity in cold‐temperate areas of the Northern Hemisphere. Despite great expansion in our knowledge of the phylogenetic history of the genus and many molecular studies focusing on the biogeography of particular groups during the last few decades, a global analysis of Carex biogeography and diversification is still lacking. For this purpose, we built the hitherto most comprehensive Carex‐dated phylogeny based on three markers (ETS–ITS–matK), using a previous phylogenomic Hyb‐Seq framework, and a sampling of two‐thirds of its species and all recognized sections. Ancestral area reconstruction, biogeographic stochastic mapping, and diversification rate analyses were conducted to elucidate macroevolutionary biogeographic and diversification patterns. Our results reveal that Carex originated in the late Eocene in E Asia, where it probably remained until the synchronous diversification of its main subgeneric lineages during the late Oligocene. E Asia is supported as the cradle of Carex diversification, as well as a “museum” of extant species diversity. Subsequent “out‐of‐Asia” colonization patterns feature multiple asymmetric dispersals clustered toward present times among the Northern Hemisphere regions, with major regions acting both as source and sink (especially Asia and North America), as well as several independent colonization events of the Southern Hemisphere. We detected 13 notable diversification rate shifts during the last 10 My, including remarkable radiations in North America and New Zealand, which occurred concurrently with the late Neogene global cooling, which suggests that diversification involved the colonization of new areas and expansion into novel areas of niche space.

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Section: Discussionsupporting

confidence: 55%

A tale of worldwide success: Behind the scenes of Carex (Cyperaceae) biogeography and diversification

Martín‐Bravo

Jiménez‐Mejías

Villaverde

et al. 2019

J of Sytematics Evolution

168

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“…As expected, the Ericales formed a monophyletic group. The topology of our tree mirrors relationships recovered from a more comprehensive analysis of a supermatrix that includes nearly 5000 species and 25 loci [52]. In both analyses, the balsaminoids (represented by Impatiens piufanensis and Hydrocera triflora in our data) are placed sister to the rest of the Ericales; and the Ericaceae are sister to the sarracenioids (represented by Actinidia in our data) in a strongly supported clade.…”

Section: Phylogenetic Analysis Of V Macrocarpon and Related Speciessupporting

confidence: 57%

Pacbio sequencing reveals identical organelle genomes between American cranberry (Vaccinium macrocarponAit.) and a wild relative

Diaz‐Garcia¹,

Rodríguez-Bonilla²,

Smith

et al. 2019

Preprint

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Breeding efforts in the American cranberry (Vaccinium macrocarpon Ait.), a North American perennial fruit crop of great importance, have been hampered by the limited genetic and phenotypic variability observed among cultivars and experimental materials. Most of the cultivars commercially used by cranberry growers today were derived from a few wild accessions bred in the 1950s. In different crops, wild germplasm has been used as an important genetic resource to incorporate novel traits and increase the phenotypic diversity of breeding materials. Vaccinium microcarpum (Turcz. ex Rupr.) Schmalh. and V. oxycoccos L., two closely related species, may be cross-compatible with the American cranberry and could be useful to improve fruit quality such as phytochemical content, and given their northern distribution, could also help develop cold hardy cultivars. Although these species have previously been analyzed in diversity studies, genomic characterization and comparative studies are still lacking. In this study, we sequenced and assembled the organelle genomes of the cultivated American cranberry and its wild relative, V. microcarpum. PacBio sequencing technology allowed us to assemble both mitochondrial and plastid genomes at very high coverage and in a single circular scaffold. A comparative analysis revealed that the mitochondrial genome sequences were identical between both species and that the plastids presented only two synonymous single nucleotide polymorphisms (SNPs). Moreover, Illumina resequencing of additional accessions of V. microcarpum and V. oxycoccos revealed high genetic variation in both species. Based on these results, we provided a hypothesis involving the extension and dynamics of the last glaciation period in North America, and how this could have shaped the distribution and dispersal of V.microcarpum. Finally, we provided important data regarding the polyploid origin of V.oxycoccos.

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“…Holoparasitism has arisen at least twice in Ericales (Monotropoideae:Ericaceae, Mitrastemonaceae), as has carnivory in the American pitcher plants (Sarraceniaceae). Although the florally disparate Ericales has been a well‐recognized clade since the widespread implementation of phylogenetic methods (Chase et al., ; Anderberg et al., ; Schönenberger et al., ; Rose et al., ; Leebens‐Mack et al., ), the evolutionary relationships among major clades within Ericales remain contentious.…”

mentioning

confidence: 99%

“…Rose et al. () utilized three nuclear, nine mitochondrial, and 13 chloroplast loci in a concatenated supermatrix consisting of 49,435 aligned sites and including 4531 ericalean species but with 87.6% missing data. Despite the extensive taxon sampling utilized in Rose et al.…”

mentioning

confidence: 99%

A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales

Larson

Walker

Vargas

et al. 2020

American J of Botany

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Premise Large genomic data sets offer the promise of resolving historically recalcitrant species relationships. However, different methodologies can yield conflicting results, especially when clades have experienced ancient, rapid diversification. Here, we analyzed the ancient radiation of Ericales and explored sources of uncertainty related to species tree inference, conflicting gene tree signal, and the inferred placement of gene and genome duplications. Methods We used a hierarchical clustering approach, with tree‐based homology and orthology detection, to generate six filtered phylogenomic matrices consisting of data from 97 transcriptomes and genomes. Support for species relationships was inferred from multiple lines of evidence including shared gene duplications, gene tree conflict, gene‐wise edge‐based analyses, concatenation, and coalescent‐based methods, and is summarized in a consensus framework. Results Our consensus approach supported a topology largely concordant with previous studies, but suggests that the data are not capable of resolving several ancient relationships because of lack of informative characters, sensitivity to methodology, and extensive gene tree conflict correlated with paleopolyploidy. We found evidence of a whole‐genome duplication before the radiation of all or most ericalean families, and demonstrate that tree topology and heterogeneous evolutionary rates affect the inferred placement of genome duplications. Conclusions We provide several hypotheses regarding the history of Ericales, and confidently resolve most nodes, but demonstrate that a series of ancient divergences are unresolvable with these data. Whether paleopolyploidy is a major source of the observed phylogenetic conflict warrants further investigation.

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Phylogeny, historical biogeography, and diversification of angiosperm order Ericales suggest ancient Neotropical and East Asian connections

Cited by 103 publications

References 128 publications

A tale of worldwide success: Behind the scenes of Carex (Cyperaceae) biogeography and diversification

A tale of worldwide success: Behind the scenes of Carex (Cyperaceae) biogeography and diversification

Pacbio sequencing reveals identical organelle genomes between American cranberry (Vaccinium macrocarponAit.) and a wild relative

A consensus phylogenomic approach highlights paleopolyploid and rapid radiation in the history of Ericales

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