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5 results for “cyto-nuclear discordance”
Phylogenomic analysis of the hemp family (Cannabaceae) reveals deep cyto-nuclear discordance and provides new insights into generic relationships
<p>Cannabaceae are a relatively small family of angiosperms, but they include several species of huge economic and cultural significance: marijuana or hemp (Cannabis sativa) and hops (Humulus lupulus). Previous phylogenetic studies clarified most deep relationships in Cannabaceae, but relationships remain ambiguous among several major lineages. Here, we sampled 83 species representing all genera of Cannabaceae and utilized a new dataset of 90 nuclear genes and 82 chloroplast loci from Hyb-Seq to investigate the phylogenomics of Cannabaceae. Nuclear phylogenetic analyses revealed a robust and consistent backbone for Cannabaceae. We observed nuclear gene-tree conflict at several deep nodes in inferred species trees, also cyto-nuclear discordance concerning the relationship between Gironniera and Lozanella and the relationships among Trema s.l. (including Parasponia), Cannabis + Humulus, and Chaetachme + Pteroceltis. Coalescent simulations and network analyses suggest that observed deep cyto-nuclear discordances likeliest stem from incomplete lineage sorting (ILS); nuclear gene-tree conflict might be caused by both ILS and gene flow between species. All genera of Cannabaceae were recovered as monophyletic, except for Celtis, which consisted of two distinct clades: Celtis I (including most Celtis species) and Celtis II (including Celtis gomphophylla and Celtis schippii). We suggest that Celtis II should be recognized as the independent genus Sparrea based on both molecular and morphological evidence. Our work provides the most comprehensive and reliable phylogeny to date for Cannabaceae, enabling further exploration of evolutionary patterns across this family and highlighting the necessity of comparing nuclear with chloroplast data to examine the evolutionary history of plant groups.</p>
Phylogenomic analysis of the hemp family (Cannabaceae) reveals deep cyto-nuclear discordance and provides new insights into generic relationships
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Data from: First plastid phylogenomic study reveals potential cyto-nuclear discordance in the evolutionary history of Ficus L. (Moraceae)
Standard Sanger chloroplast markers provide limited information to resolve species level relationships within plants, in particular within large genera. Figs (Ficus L., Moraceae) compose one of the 50 largest genera of angiosperms with ∼750 species occurring in the tropics and subtropics worldwide. Figs, in addition to being a keystone food resource in rainforests, are well-known for the mutualistic interactions with their pollinating wasps. It is regarded as a model system for understanding co-evolution dating back more than 75 million years. However, despite significant taxon sampling, combinations of low copy nuclear, nuclear ribosomal and chloroplast regions have not been able to confidently resolve relationships among major groups of figs. Using a high throughput sequencing approach we attempted to resolve the major lineages of Ficus based on plastome data. In this study, we show that the use of a de novo assembled plastome from within the genus provides less ambiguity and higher coverage across the 59 Ficus and 6 outgroup plastome assemblies compared to using the nearest available reference plastome outside the genus resulting in improved resolution and higher support of the phylogenetic relationships within Ficus inferred from plastome data. Chloroplast genome data confidently resolved relationships among major groups of figs and largely support current understanding based on nuclear sequence data including passively pollinated Neotropical section Pharmacosycea as sister lineage to all other Ficus. However, conflicts between the new plastome topology and previous nuclear studies are observed for both individual species as well as relationships among some sections at deeper levels. Conflicts could be caused by lack of resolution in the nuclear data or may indicate potential cyto-nuclear discordance as previously observed in an African lineage of Ficus.
Data from: First plastid phylogenomic study reveals potential cyto-nuclear discordance in the evolutionary history of Ficus L. (Moraceae)
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Data from: Hybridization during altitudinal range shifts: nuclear introgression leads to extensive cyto-nuclear discordance in the fire salamander
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