Population Genomics of Endemic Species

Population genomics of endemic species combines high-throughput sequencing and population-level sampling to characterise patterns of genetic variation within organisms confined to restricted geographic ranges. By analysing thousands to millions of single nucleotide polymorphisms (SNPs) or microsatellite loci, researchers can infer demographic history, gene flow, inbreeding, local adaptation and the impact of historical climatic or geological events on isolated populations. These approaches reveal how mountain uplift, glacial oscillations, island formation and habitat fragmentation have shaped genetic structure and speciation in biodiversity hotspots. Insights from population genomics underpin evidence-based conservation, guiding the design of protected areas, ex situ breeding programmes and biosecurity measures to preserve evolutionary potential in the face of global change.

Research from Nature Portfolio

Analyses of narrow endemics in Mediterranean mountain refugia have employed microsatellite genotyping alongside ecological niche modelling to reconstruct post-glacial dynamics. Seven centaurea taxa from Anatolian mountains exhibited moderate to high genetic diversity despite their restricted ranges. Genetic clusters correspond to past refugial corridors active during glacial maxima, while modern populations show pronounced isolation. This work demonstrates how historical connectivity and subsequent allopatric divergence in complex orography maintain high diversity in plant endemics and drive speciation.

Population Genomics of Endemic Species publication trend

The graph below shows the total number of articles in population genomics of endemic species across all publications each year (not limited to Nature Index journals).

Technical terms

Single nucleotide polymorphism (SNP): A single-base variation in the genome used as a genetic marker to assess diversity and population structure.

Microsatellite (SSR): A tandem repeat of short DNA motifs, highly polymorphic and useful for analysing fine-scale genetic variation.

Reduced-representation sequencing: A method (e.g. ddRADseq) that samples a reproducible subset of the genome to identify polymorphisms cost-effectively.

Effective population size (Ne): The size of an idealised population that would experience the same rate of genetic drift as the observed population.

Ecological niche modelling: A computational approach that predicts the past, present or future distribution of species based on environmental variables and occurrence records.

Allopatric divergence: The evolutionary process by which populations become genetically distinct due to geographic isolation.

References

1. Speciation and genetic diversity in Centaurea subsect. Phalolepis in Anatolia. Scientific Reports (2016).
2. One Step Away From Extinction: A Population Genomic Analysis of A Narrow Endemic, Tropical Plant Species. Frontiers in Plant Science (2021).
3. Conservation implications of genetic structure in the narrowest endemic quillwort from the Eastern Amazon. Ecology and Evolution (2021).
4. Localized environmental heterogeneity drives the population differentiation of two endangered and endemic Opisthopappus Shih species. BMC Ecology and Evolution (2021).