Phylogenetic Analysis Using Next-Generation Sequencing

Next-generation sequencing (NGS) technologies have revolutionised phylogenetic analysis by enabling the acquisition of genome-scale data. Phylogenetic inference reconstructs evolutionary relationships by leveraging datasets generated through whole-genome resequencing, reduced-representation methods such as RAD sequencing, transcriptome assembly and organellar genome recovery. These approaches yield vast numbers of orthologous markers across diverse taxa, improving resolution at both deep and recent divergences. Sophisticated bioinformatic pipelines assemble short reads into loci, partition data by gene or genomic region, and apply maximum likelihood or Bayesian frameworks to infer species trees. Advances in discordance analysis, exemplified by quartet sampling, allow researchers to disentangle genuine topological conflicts from lack of support, addressing challenges posed by incomplete lineage sorting, introgression and gene duplication. The integration of NGS-based phylogenetics has driven breakthroughs in plant systematics, animal conservation, microbial ecology and epidemiology. For instance, genome-wide markers have clarified cryptic species boundaries in endangered amphibians, while transcriptome sequencing of museum specimens is widening geographical and taxonomic sampling. The global significance of these developments spans from informing conservation prioritisation to tracing pathogen outbreaks, illustrating the transformative impact of high-throughput sequencing on our understanding of the tree of life.

Research from Nature Portfolio

Recent studies have employed genome-wide nuclear markers to elucidate phylogenetic relationships within an endangered amphibian, revealing distinct evolutionary lineages and informing conservation strategies. By analysing over a thousand loci using high-throughput sequencing, researchers identified reproductive isolation and historical gene-flow patterns among nearctic populations. This work led to the designation of discrete management units, each requiring tailored habitat restoration and captive propagation plans. These findings underscore the value of deep-coverage genomic data for resolving fine-scale divergences and guiding practical interventions for at-risk species.

Research from all publishers

Innovative work has demonstrated the feasibility of sequencing historical RNA from preserved plant specimens, overcoming traditional cold-chain limitations and enabling transcriptome assembly from century-old material. This approach promises to fill geographic and taxonomic gaps in the plant tree of life and supports broader sampling of herbarium collections. Another study compared chloroplast and mitochondrial genomes across hundreds of land plants, uncovering largely concordant phylogenies yet highlighting specific regions of conflict arising from divergent rates of molecular evolution. These insights emphasise the need for tailored evolutionary models for organellar datasets and showcase the nuanced information that comprehensive organelle sequencing can contribute to phylogenetics.

Phylogenetic Analysis Using Next-Generation Sequencing publication trend

The graph below shows the total number of articles in phylogenetic analysis using next-generation sequencing across all publications each year (not limited to Nature Index journals).

Technical terms

Next-generation sequencing (NGS): High-throughput methods for rapid DNA or RNA sequencing, producing large volumes of short reads for genomic analysis.

Phylogenetic inference: Computational reconstruction of evolutionary relationships among species based on genetic data.

Transcriptome sequencing: Sequencing of the complete set of RNA transcripts to capture expressed genes across tissues or specimens.

Organellar genome: The genetic material of mitochondria or chloroplasts, often used as a phylogenetic marker due to distinct inheritance and mutation rates.

Restriction-site associated DNA sequencing (RAD-Seq): A reduced-representation method that targets genomic regions flanking restriction enzyme sites to generate hundreds to thousands of markers.

Admixture analysis: Statistical assessment of historical gene flow and population structure by estimating ancestral contributions to individual genomes.

Management unit: A population segment distinguished by genetic data for targeted conservation and management efforts.

References

1. Sequencing historical RNA: unrealized potential to increase understanding of the plant tree of life. Trends in Plant Science (2024).
2. Characterizing conflict and congruence of molecular evolution across organellar genome sequences for phylogenetics in land plants. Frontiers in Plant Science (2023).
3. Using genome-wide data to ascertain taxonomic status and assess population genetic structure for Houston toads (Bufo [= Anaxyrus] houstonensis). Scientific Reports (2024).
4. Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life. American Journal of Botany (2018).