A robust phylogenomic framework for the calamoid palms

Kuhnhäuser, Benedikt G.; Bellot, Sidonie; Couvreur, Thomas L.P.; Dransfield, John; Henderson, Andrew; Schley, Rowan J.; Chomicki, Guillaume; Eiserhardt, Wolf L.; Hiscock, Simon J.; Baker, William J.

doi:10.1016/j.ympev.2020.107067

Cited by 18 publications

(25 citation statements)

References 75 publications

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“…The relationships between lineages, including extant taxa, were poorly supported. This lack of support is most likely owing to insufficient morphological and molecular information and recent phylogenomic trees at larger phylogenetic scale have obtained better resolution [32,33]. We performed all analyses on a posterior distribution of trees to account for phylogenetic uncertainty.…”

Section: Resultsmentioning

confidence: 99%

The origin of modern patterns of continental diversity in Mauritiinae palms: the Neotropical museum and the Afrotropical graveyard

et al. 2022

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While the latitudinal diversity gradient has received much attention, biodiversity and species richness also vary between continents across similar latitudes. Fossil information can be used to understand the evolutionary mechanisms that generated such variation between continents of similar latitudes. We integrated fossil data into a phylogenetic analysis of the Mauritiinae palms, whose extant diversity is restricted to the Neotropics, but extended across Africa and India during most of the Cenozoic. Mauritiinae diverged from its sister lineage Raphiinae ca 106 Ma. Using ancestral state estimation and a lineage through time analysis, we found that diversity arose globally during the late Cretaceous and Palaeocene across South America, Africa and India. The Palaeocene–Eocene transition ( ca 56 Ma) marked the end of global Mauritiinae expansion, and the beginning of their decline in both Africa and India. Mauritiinae disappeared from the Indian subcontinent and Africa at the end of the Eocene and the Miocene, respectively. By contrast, Neotropical diversity steadily increased over the last 80 Myr. Taken together, our results suggest that the Neotropics functioned as a continental-scale refuge for Mauritiinae palms, where lineages survived and diversified while global climatic changes that drastically reduced rainforests led to their demise on other continents.

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Section: Resultsmentioning

confidence: 99%

The origin of modern patterns of continental diversity in Mauritiinae palms: the Neotropical museum and the Afrotropical graveyard

et al. 2022

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“…Hence, both over- and underestimation of the number of detected putative paralogs is a possible outcome. Another common approach to deal with paralogs is to exclude entire genes that show evidence of paralogy, e.g., by removing putatively paralogous genes flagged by HybPiper (e.g., Larridon et al, 2020 ; Christe et al, 2021 ; Kuhnhäuser et al, 2021 ). Here, this approach resulted in a severe reduction of available sequence data left for species tree inference, which is common when many species are sampled ( Emms and Kelly, 2018 ; Jones et al, 2019 ).…”

Section: Discussionmentioning

confidence: 99%

Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae)

et al. 2022

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Subfamily Rubioideae is the largest of the main lineages in the coffee family (Rubiaceae), with over 8,000 species and 29 tribes. Phylogenetic relationships among tribes and other major clades within this group of plants are still only partly resolved despite considerable efforts. While previous studies have mainly utilized data from the organellar genomes and nuclear ribosomal DNA, we here use a large number of low-copy nuclear genes obtained via a target capture approach to infer phylogenetic relationships within Rubioideae. We included 101 Rubioideae species representing all but two (the monogeneric tribes Foonchewieae and Aitchinsonieae) of the currently recognized tribes, and all but one non-monogeneric tribe were represented by more than one genus. Using data from the 353 genes targeted with the universal Angiosperms353 probe set we investigated the impact of data type, analytical approach, and potential paralogs on phylogenetic reconstruction. We inferred a robust phylogenetic hypothesis of Rubioideae with the vast majority (or all) nodes being highly supported across all analyses and datasets and few incongruences between the inferred topologies. The results were similar to those of previous studies but novel relationships were also identified. We found that supercontigs [coding sequence (CDS) + non-coding sequence] clearly outperformed CDS data in levels of support and gene tree congruence. The full datasets (353 genes) outperformed the datasets with potentially paralogous genes removed (186 genes) in levels of support but increased gene tree incongruence slightly. The pattern of gene tree conflict at short internal branches were often consistent with high levels of incomplete lineage sorting (ILS) due to rapid speciation in the group. While concatenation- and coalescence-based trees mainly agreed, the observed phylogenetic discordance between the two approaches may be best explained by their differences in accounting for ILS. The use of target capture data greatly improved our confidence and understanding of the Rubioideae phylogeny, highlighted by the increased support for previously uncertain relationships and the increased possibility to explore sources of underlying phylogenetic discordance.

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“…Our study adds to a growing list of palm clades in which phylogenomic methods have yielded a much improved systematic framework (e.g., Heyduk & al., 2016; Loiseau & al., 2019; Helmstetter & al., 2020; Jiménez & al., 2021; Kuhnhäuser & al., 2021). Our results clearly illustrate the value of a target sequence capture approach including loci from across the genome.…”

Section: Discussionmentioning

confidence: 99%

Phylogenomics and generic limits of Dypsidinae (Arecaceae), the largest palm radiation in Madagascar

Eiserhardt

Bellot

Cowan

et al. 2022

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With 178 species, palm subtribe Dypsidinae is one of the largest plant radiations on Madagascar. A well-resolved species-level phylogeny is required not only to unpick the drivers of this spectacular radiation, but also to define natural and useful generic limits in this taxonomically difficult group. The only recent taxonomic revision of Dypsidinae recognised just four genera, including the large genus Dypsis (currently with 172 species), which was considered impossible to divide further based on morphology alone. Here we describe the first comprehensively sampled species-level phylogeny of Dypsidinae, including 157 described species (88% of the subtribe) as well as 10 samples of uncertain taxonomic identity (potentially new to science). Our tree is based on target sequence capture data for 161 nuclear DNA loci. The phylogenetic relationships recovered render Dypsis s.l. paraphyletic, requiring the resurrection of two previously synonymised genera. In total, we recognise six genera in Dypsidinae (Dypsis, Chrysalidocarpus, Marojejya, Vonitra, Lemurophoenix, Masoala), all of which are monophyletic and consistent with morphology.

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A robust phylogenomic framework for the calamoid palms

Cited by 18 publications

References 75 publications

The origin of modern patterns of continental diversity in Mauritiinae palms: the Neotropical museum and the Afrotropical graveyard

The origin of modern patterns of continental diversity in Mauritiinae palms: the Neotropical museum and the Afrotropical graveyard

Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae)

Phylogenomics and generic limits of Dypsidinae (Arecaceae), the largest palm radiation in Madagascar

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