Phylogenomic Analysis of Aceraceae and Related Taxa

The Aceraceae, now usually included within Sapindaceae, encompass the maples and their closest relatives, a group renowned for ecological importance, ornamental value and complex taxonomy. Phylogenomic approaches, which integrate data from entire plastid genomes and hundreds of nuclear markers, have transformed our understanding of species boundaries, sectional relationships and historical biogeography within Acer and allied genera such as Dipteronia and Koelreuteria. By combining high‐throughput sequencing, rigorous alignment of coding and non-coding regions and coalescent‐based inference, researchers have disentangled the effects of hybridisation, incomplete lineage sorting and chloroplast capture that have long confounded morphology-based classifications. These studies have yielded robust phylogenetic backbones, revealed inter- and intraspecific cytonuclear discordance, and elucidated patterns of diversification linked to climatic shifts since the Miocene. The resulting framework has broad implications for conservation prioritisation, molecular breeding and the reconstruction of Northern Hemisphere forest dynamics under past and future environmental change.

Research from Nature Portfolio

One comprehensive analysis reconstructed the phylogeny and biogeographic history of maples using a combination of nuclear internal transcribed spacer sequences and three chloroplast markers. Phylogenetic trees generated by maximum likelihood, maximum parsimony and Bayesian methods consistently placed the centre of origin in Asia. Multiple independent dispersal events across the Bering and North Atlantic land bridges were inferred, with intercontinental migrations occurring predominantly in the Miocene. This work provides a clear demonstration of how geological connectivity and climatic fluctuations shaped the modern distribution of Aceraceae and offers a model for studying the assembly of temperate forest flora.

Phylogenomic Analysis of Aceraceae and Related Taxa publication trend

The graph below shows the total number of articles in phylogenomic analysis of aceraceae and related taxa across all publications each year (not limited to Nature Index journals).

Technical terms

Phylogenomics: Integrative analysis of genome‐scale data to infer evolutionary relationships among organisms.

Plastome: Complete DNA sequence of a plastid, typically the chloroplast, widely used for reconstructing plant phylogenies.

Nuclear ribosomal DNA (nrDNA): Tandemly repeated nuclear genes encoding ribosomal RNA, serving as molecular markers for species identification and phylogenetic inference.

Incomplete lineage sorting (ILS): Retention of ancestral genetic variants in descendant lineages, leading to discordant gene trees.

Chloroplast capture: Introgression of a plastid genome from one species into another via hybridisation, resulting in mismatches between nuclear and plastid phylogenies.

Cytonuclear discordance: Conflict between phylogenetic signals from cytoplasmic (plastid or mitochondrial) and nuclear genomes, often reflecting hybridisation or ILS.

References

1. Historical biogeography of Acer L. (Sapindaceae): genetic evidence for Out-of-Asia hypothesis with multiple dispersals to North America and Europe. Scientific Reports (2020).
2. Testing plastomes and nuclear ribosomal DNA sequences as the next-generation DNA barcodes for species identification and phylogenetic analysis in Acer. BMC Plant Biology (2024).
3. Insights Into Comparative Analyses and Phylogenomic Implications of Acer (Sapindaceae) Inferred From Complete Chloroplast Genomes. Frontiers in Genetics (2022).
4. Plastome comparative genomics in maples resolves the infrageneric backbone relationships. PeerJ (2020).